6C1Q | pdb_00006c1q

Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist NDT9513727

External Resource: Annotation

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
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Cytochromes	8057879	3001526	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	G protein-coupled receptor-like	8091170	3000473	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	7tm_1_1	e6c1qB1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: 7tm_1_1	ECOD (1.6)
A [auth B]	Cytochrom_B562_1	e6c1qB2	A: alpha bundles	X: Four-helical up-and-down bundle	H: Cytochromes (From Topology)	T: Cytochromes	F: Cytochrom_B562_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	1.20.120.10	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Cytochrome c/b562	CATH (utative)
A [auth B]	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF07361	Cytochrome b562 (Cytochrom_B562)	Cytochrome b562	-	Family
A [auth B]	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GC ...	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding opsonin receptor activity molecular transducer activity complement receptor activity transmembrane signaling receptor activity binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding opsonin receptor activity molecular transducer activity complement receptor activity transmembrane signaling receptor activity signaling receptor activity complement component C5a receptor activity immune receptor activity G protein-coupled receptor activity	electron transport chain metabolic process cellular process generation of precursor metabolites and energy positive regulation of cytosolic calcium ion concentration biological regulation regulation of biological quality cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process electron transport chain metabolic process cellular process generation of precursor metabolites and energy positive regulation of cytosolic calcium ion concentration biological regulation regulation of biological quality cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling multicellular organismal process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression vascular endothelial growth factor production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process cellular component organization cell junction organization presynapse organization synapse organization cellular component organization or biogenesis immune response immune system process immune response-regulating cell surface receptor signaling pathway complement receptor mediated 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 regulation of immune response activation of immune response amyloid-beta clearance cell chemotaxis chemotaxis neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis granulocyte chemotaxis response to chemical myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion system process nervous system process cognition cell population proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of locomotion regulation of cell motility positive regulation of chemotaxis positive regulation of cell migration positive regulation of neutrophil chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte chemotaxis positive regulation of granulocyte chemotaxis regulation of locomotion regulation of neutrophil chemotaxis regulation of neutrophil migration regulation of response to external stimulus regulation of granulocyte chemotaxis positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration positive regulation of leukocyte migration positive regulation of neutrophil migration regulation of chemotaxis macrophage migration regulation of mononuclear cell migration positive regulation of macrophage migration macrophage chemotaxis regulation of macrophage migration positive regulation of mononuclear cell migration regulation of macrophage chemotaxis mononuclear cell migration positive regulation of macrophage chemotaxis cellular developmental process astrocyte differentiation cell development astrocyte activation glial cell development multicellular organism development neurogenesis astrocyte development gliogenesis cell differentiation response to stress anatomical structure development system development developmental process defense response cell activation nervous system development central nervous system development glial cell differentiation glial cell activation inflammatory response neuroinflammatory response regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis complement component C5a signaling pathway G protein-coupled receptor signaling pathway phospholipase C-activating G protein-coupled receptor signaling pathway mRNA transcription by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process mRNA transcription mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II cellular defense response sensory perception of chemical stimulus sensory perception biological process involved in interspecies interaction between organisms response to other organism response to oxygen-containing compound response to nitrogen compound response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin response to peptidoglycan myeloid leukocyte activation leukocyte activation macrophage activation leukocyte activation involved in inflammatory response microglial cell activation defense response to Gram-positive bacterium defense response to bacterium	cellular anatomical structure periplasmic space apical part of cell cell periphery plasma membrane membrane basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle cellular anatomical structure periplasmic space apical part of cell cell periphery plasma membrane membrane basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane
B [auth L]	PMX53	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR010980	Cytochrome c/b562	Homologous Superfamily
A [auth B]	IPR009155	Cytochrome b562	Family
A [auth B]	IPR002234	Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2	Family
A [auth B]	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A [auth B]	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A [auth B]	IPR000826	Formyl peptide receptor-related	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	Pharos: P21730	toxic shock syndrome Liver Cirrhosis, Experimental MALT lymphoma osteosarcoma psoriasis adrenal cortex carcinoma B-cell chronic lymphocytic leukemia gastric cancer granulomatosis with polyangiitis invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer ulcerative colitis cutaneous lupus erythematosus toxic shock syndrome Liver Cirrhosis, Experimental MALT lymphoma osteosarcoma psoriasis adrenal cortex carcinoma B-cell chronic lymphocytic leukemia gastric cancer granulomatosis with polyangiitis invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer ulcerative colitis cutaneous lupus erythematosus gastric carcinoma IgA glomerulonephritis lung carcinoma malignant mesothelioma non-small cell lung carcinoma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma interstitial cystitis lung adenocarcinoma malignant ependymoma

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth B]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth B]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	C5a anaphylatoxin chemotactic receptor 1 (C5aR) in complex with orthosteric antagonist PMX53 and allosteric antagonist NDT9513727

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth B]	YCM	Parent Component: CYS
B [auth L]	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
B [auth L]	ORN	Parent Component: ALA RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
B [auth L]	ZAL	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354

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.