1LFD | pdb_00001lfd

CRYSTAL STRUCTURE OF THE ACTIVE RAS PROTEIN COMPLEXED WITH THE RAS-INTERACTING DOMAIN OF RALGDS

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1lfdd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	cH-p21 Ras protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1lfdb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	cH-p21 Ras protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1lfdc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ras-binding domain, RBD	Ral guanosine-nucleotide exchange factor, RalGDS	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1lfda_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ras-binding domain, RBD	Ral guanosine-nucleotide exchange factor, RalGDS	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8019405	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8019405	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8034482	3000157	SCOP2B (2022-06-29)
A	SCOP2 Family	Ras-binding domain, RBD	8022102	4000380	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ubiquitin-like	8034482	3000157	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Ras	e1lfdD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
B	Ras	e1lfdB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
C	RA	e1lfdC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RA	ECOD (1.6)
A	RA	e1lfdA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motili ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain
A, C	PF00788	Ras association (RalGDS/AF-6) domain (RA)	Ras association (RalGDS/AF-6) domain	RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure [3] similar to that determined [1], and that of th ...	RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure [3] similar to that determined [1], and that of the RasGTP-binding domain of Raf kinase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	RAS	pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity enzyme regulator activity enzyme activator activity phospholipase C activator activity molecular function activator activity phospholipase activator activity molecular function regulator activity lipase activator activity pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity enzyme regulator activity enzyme activator activity phospholipase C activator activity molecular function activator activity phospholipase activator activity molecular function regulator activity lipase activator activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity G protein activity	positive regulation of response to wounding wound healing regulation of biological process response to stimulus biological regulation positive regulation of biological process regulation of response to wounding positive regulation of response to stimulus positive regulation of wound healing regulation of response to stimulus response to stress regulation of response to stress regulation of wound healing response to wounding positive regulation of response to wounding wound healing regulation of biological process response to stimulus biological regulation positive regulation of biological process regulation of response to wounding positive regulation of response to stimulus positive regulation of wound healing regulation of response to stimulus response to stress regulation of response to stress regulation of wound healing response to wounding regulation of cellular process RNA metabolic process positive regulation of miRNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process positive regulation of cellular process primary metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of RNA metabolic process cellular process metabolic process macromolecule metabolic process regulation of metabolic process cellular response to stimulus cellular response to stress cellular senescence signaling intracellular signal transduction cell communication intracellular signaling cassette MAPK cascade signal transduction chemotaxis taxis response to chemical response to external stimulus locomotion regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling regulation of signaling regulation of long-term neuronal synaptic plasticity modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of biological quality positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade positive regulation of signaling biological process involved in interspecies interaction between organisms response to other organism defense response defense response to protozoan response to biotic stimulus response to protozoan defense response to other organism response to external biotic stimulus fibroblast proliferation cell population proliferation positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription transcription by RNA polymerase II positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of localization cellular localization establishment of protein localization regulation of protein localization protein targeting positive regulation of establishment of protein localization localization regulation of protein targeting to membrane intracellular protein localization establishment of protein localization to membrane regulation of establishment of protein localization localization within membrane establishment of localization protein targeting to membrane regulation of cellular localization regulation of protein targeting macromolecule localization positive regulation of protein targeting to membrane regulation of cellular component organization positive regulation of cellular component organization cell projection organization ruffle organization plasma membrane bounded cell projection assembly ruffle assembly cellular component biogenesis cellular component organization cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis positive regulation of ruffle assembly regulation of plasma membrane bounded cell projection assembly regulation of ruffle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly developmental process connective tissue development adipose tissue development animal organ development anatomical structure development tissue development immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response anatomical structure morphogenesis animal organ morphogenesis positive regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade cell death apoptotic signaling pathway apoptotic process intrinsic apoptotic signaling pathway programmed cell death cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus response to gamma radiation import into cell transport endocytosis vesicle-mediated transport regulation of cytoskeleton organization regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cytoskeleton organization positive regulation of cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation multicellular organismal process cellular developmental process peripheral nervous system development cell development nervous system development glial cell development multicellular organism development neurogenesis Schwann cell development gliogenesis glial cell differentiation cell differentiation Schwann cell differentiation system development positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process regulation of neuron apoptotic process small GTPase-mediated signal transduction Ras protein signal transduction protein localization to synapse regulation of neurotransmitter receptor localization to postsynaptic specialization membrane regulation of protein localization to synapse neurotransmitter receptor localization to postsynaptic specialization membrane regulation of protein localization to membrane regulation of receptor localization to synapse protein localization to postsynaptic specialization membrane protein localization to cell periphery protein localization to postsynaptic membrane regulation of protein localization to cell periphery protein localization to membrane protein-containing complex localization regulation of postsynaptic membrane neurotransmitter receptor levels protein localization to organelle protein localization to postsynapse protein localization to cell junction receptor localization to synapse oncogene-induced cell senescence cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus response to endogenous stimulus response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to insulin cellular response to insulin stimulus negative regulation of cell population proliferation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains T-helper 1 type immune response adaptive immune response myelination axon ensheathment ensheathment of neurons cell cycle regulation of cell cycle negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process regulation of type II interferon production type II interferon production cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of type II interferon production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system Golgi membrane cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system Golgi membrane membrane bounding membrane of organelle organelle membrane perinuclear region of cytoplasm intracellular membraneless organelle cilium plasma membrane bounded cell projection ciliary basal body cell projection microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane protein-containing complex catalytic complex GTPase complex
A, C	RALGDS	GTPase regulator activity enzyme regulator activity nucleoside-triphosphatase regulator activity molecular function regulator activity guanyl-nucleotide exchange factor activity	cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication intracellular signaling cassette cellular process signal transduction Ras protein signal transduction	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane apical part of cell cluster of actin-based cell projections brush border membrane-bounded organelle intracellular organelle organelle nucleus cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane apical part of cell cluster of actin-based cell projections brush border membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D	IPR020849	Small GTPase, Ras-type	Family
B, D	IPR005225	Small GTP-binding domain	Domain
B, D	IPR001806	Small GTPase	Family
A, C	IPR000159	Ras-associating domain	Domain
A, C	IPR008937	Ras-like guanine nucleotide exchange factor	Family
A, C	IPR019804	Ras guanine-nucleotide exchange factor, conserved site	Conserved Site
A, C	IPR000651	Ras-like guanine nucleotide exchange factor, N-terminal	Domain
A, C	IPR036964	Ras guanine-nucleotide exchange factor, catalytic domain superfamily	Homologous Superfamily
A, C	IPR015758	Ral guanine nucleotide dissociation stimulator, RA domain	Domain
A, C	IPR023578	Ras guanine nucleotide exchange factor domain superfamily	Homologous Superfamily
A, C	IPR001895	Ras guanine-nucleotide exchange factors catalytic domain	Domain
A, C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: P01112	Costello syndrome urinary bladder cancer thyroid cancer, nonmedullary, 2 cardiofaciocutaneous syndrome Noonan syndrome cancer transitional cell carcinoma large congenital melanocytic nevus seminoma squamous cell carcinoma hepatocellular adenoma angiosarcoma neuroblastoma nevus, epidermal penile neoplasm Costello syndrome urinary bladder cancer thyroid cancer, nonmedullary, 2 cardiofaciocutaneous syndrome Noonan syndrome cancer transitional cell carcinoma large congenital melanocytic nevus seminoma squamous cell carcinoma hepatocellular adenoma angiosarcoma neuroblastoma nevus, epidermal penile neoplasm sarcomatoid carcinoma breast carcinoma thyroid gland carcinoma carcinoma Mammary Neoplasms, Experimental salivary gland adenoid cystic carcinoma liver cancer skin neoplasm prostate cancer linear nevus sebaceus syndrome adenoid cystic carcinoma skin cancer squamous papilloma testicular seminoma thyroid adenoma papilloma head and neck squamous cell carcinoma hepatocellular carcinoma mammary neoplasms, animal hereditary diffuse gastric adenocarcinoma melanoma cervical carcinoma prostate disease hypertrophic cardiomyopathy myositis intellectual disability acute myeloid leukemia urothelial carcinoma connective tissue disease rheumatoid arthritis liver neoplasm adenoma uterine disease cutaneous melanoma lung benign neoplasm skin disease epidermal nevus syndrome bladder carcinoma in situ systemic lupus erythematosus ovarian cancer gastric cancer thymic carcinoma thyroid cancer papillomatosis hematologic disease phakomatosis pigmentokeratotica tongue cancer Hutchinson-Gilford progeria syndrome Charcot-Marie-Tooth disease hypothyroidism urinary bladder carcinoma congenital anemia verrucous nevus lung cancer astrocytic tumor lymphatic system disease brain cancer oral cavity neoplasm systemic sclerosis thymus neoplasm breast adenocarcinoma ovarian disease gastric neoplasm breast disease penile cancer thyroid gland papillary carcinoma precancerous condition cerebral cortical dysplasia hydrops fetalis undifferentiated carcinoma colorectal adenocarcinoma inflammatory linear verrucous epidermal nevus urinary bladder neoplasm rhabdomyosarcoma uterine cervix carcinoma in situ sarcoma lung adenocarcinoma woolly hair nevus digestive system disease lung disease autism endometriosis spleen cancer bladder benign neoplasm breast cancer

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.