8KC9 | pdb_00008kc9

Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to cyclosporin A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Cyclophilin-like	8042788	3000168	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13640	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy_3)	2OG-Fe(II) oxygenase superfamily	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1].	Domain
C	PF00160	Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD (Pro_isomerase)	Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD	The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond pr ...	The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Prolyl 3-hydroxylase 1	oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen procollagen-proline 3-dioxygenase activity peptidyl-proline 3-dioxygenase activity procollagen-proline dioxygenase activity peptidyl-proline dioxygenase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity organic acid binding binding carbohydrate binding vitamin binding oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen procollagen-proline 3-dioxygenase activity peptidyl-proline 3-dioxygenase activity procollagen-proline dioxygenase activity peptidyl-proline dioxygenase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity organic acid binding binding carbohydrate binding vitamin binding ion binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding small molecule binding cation binding transition metal ion binding iron ion binding metal ion binding	regulation of protein stability biological regulation regulation of biological quality protein stabilization protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation regulation of protein stability biological regulation regulation of biological quality protein stabilization protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation negative regulation of post-translational protein modification regulation of cellular process regulation of protein modification process negative regulation of biological process regulation of primary metabolic process negative regulation of protein modification process negative regulation of cellular process protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process macromolecule modification post-translational protein modification regulation of metabolic process regulation of localization establishment of protein localization nitrogen compound transport regulation of protein localization transport protein localization to extracellular region localization regulation of secretion by cell secretion by cell intracellular protein localization regulation of transport secretion regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion establishment of localization regulation of protein secretion regulation of secretion protein transport macromolecule localization protein hydroxylation developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development animal organ development bone development system development ossification regulation of multicellular organismal process regulation of ossification regulation of growth regulation of cellular component organization growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth cellular component organization or biogenesis collagen fibril organization extracellular matrix organization extracellular structure organization external encapsulating structure organization regulation of neuron projection development positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development neurogenesis neuron differentiation positive regulation of neuron projection development cell differentiation positive regulation of cell projection organization positive regulation of cellular process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation collagen metabolic process	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm protein-containing complex cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm protein-containing complex membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen endoplasmic reticulum nucleus
B	Cartilage-associated protein	-	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of protein stability biological regulation regulation of biological quality protein stabilization negative regulation of post-translational protein modification regulation of cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of protein stability biological regulation regulation of biological quality protein stabilization negative regulation of post-translational protein modification regulation of cellular process regulation of protein modification process negative regulation of biological process regulation of primary metabolic process negative regulation of protein modification process negative regulation of cellular process protein metabolic process protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process cellular process macromolecule metabolic process post-translational protein modification regulation of metabolic process cellular component organization collagen fibril organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region extracellular space protein-containing complex
C	Peptidyl-prolyl cis-trans isomerase B	isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity RNA polymerase binding protein binding binding enzyme binding RNA binding nucleic acid binding unfolded protein binding amide binding cyclosporin A binding	regulation of protein stability biological regulation regulation of biological quality protein stabilization host-mediated activation of viral genome replication biological process involved in interspecies interaction between organisms host-mediated perturbation of viral genome replication host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process host-mediated activation of viral process protein folding biosynthetic process metabolic process regulation of protein stability biological regulation regulation of biological quality protein stabilization host-mediated activation of viral genome replication biological process involved in interspecies interaction between organisms host-mediated perturbation of viral genome replication host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process host-mediated activation of viral process protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development animal organ development bone development system development cell chemotaxis cellular response to stimulus chemotaxis response to stimulus neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis response to chemical myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion regulation of multicellular organism growth regulation of biological process regulation of growth regulation of developmental growth regulation of developmental process developmental growth growth positive regulation of biological process positive regulation of multicellular organism growth positive regulation of developmental process multicellular organism growth positive regulation of growth positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of developmental growth	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endoplasmic reticulum smooth endoplasmic reticulum endomembrane system nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex endoplasmic reticulum lumen perinuclear region of cytoplasm endoplasmic reticulum chaperone complex endoplasmic reticulum protein-containing complex
D [auth E]	DSN-MLE-MLE-MVA-BMT-ABA-SAR-MLE-VAL-MLE-ALA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A	IPR056585	Leprecan-like alpha-helical domain	Domain
A	IPR044862	Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain	Domain
A	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A	IPR039575	Prolyl 3-hydroxylase	Family
B	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
B	IPR052284	Collagen-modifying leprecan protein	Family
B	IPR056585	Leprecan-like alpha-helical domain	Domain
C	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
C	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain	Domain
C	IPR020892	Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q32P28	osteogenesis imperfecta osteogenesis imperfecta type 8 osteogenesis imperfecta type 3 atypical teratoid rhabdoid tumor intellectual disability non-small cell lung carcinoma Osteogenesis imperfecta, type VIII pituitary cancer dentinogenesis imperfecta large cell medulloblastoma osteosarcoma glioblastoma osteogenesis imperfecta type 2 ovarian cancer
B	Pharos: O75718	osteogenesis imperfecta osteogenesis imperfecta type 7 osteogenesis imperfecta type 3 Liver Cirrhosis, Experimental osteogenesis imperfecta type 4 oligodendroglioma osteogenesis imperfecta type 2 osteosarcoma allergic rhinitis pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor psoriasis dentinogenesis imperfecta endogenous depression large cell medulloblastoma osteogenesis imperfecta osteogenesis imperfecta type 7 osteogenesis imperfecta type 3 Liver Cirrhosis, Experimental osteogenesis imperfecta type 4 oligodendroglioma osteogenesis imperfecta type 2 osteosarcoma allergic rhinitis pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor psoriasis dentinogenesis imperfecta endogenous depression large cell medulloblastoma lung cancer medulloblastoma osteochondrodysplasia ovarian cancer asthma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast carcinoma subependymal giant cell astrocytoma diabetes mellitus glioblastoma malignant ependymoma mucopolysaccharidosis type 4 pancreatic intraductal papillary-mucinous carcinoma atopic eczema pilocytic astrocytoma breast fibroadenoma ductal breast carcinoma in situ invasive ductal breast carcinoma malignant glioma
C	Pharos: P23284	osteogenesis imperfecta osteogenesis imperfecta type 9 osteogenesis imperfecta type 3 HIV infectious disease osteogenesis imperfecta type 4 myopathy osteogenesis imperfecta type 2 ovarian cancer plasma cell myeloma astrocytic tumor Prevention of Liver Transplant Rejection Crohn disease Duchenne muscular dystrophy limb-girdle muscular dystrophy malignant ependymoma osteogenesis imperfecta osteogenesis imperfecta type 9 osteogenesis imperfecta type 3 HIV infectious disease osteogenesis imperfecta type 4 myopathy osteogenesis imperfecta type 2 ovarian cancer plasma cell myeloma astrocytic tumor Prevention of Liver Transplant Rejection Crohn disease Duchenne muscular dystrophy limb-girdle muscular dystrophy malignant ependymoma mucocutaneous lymph node syndrome osteochondrodysplasia pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor rheumatoid arthritis dermatomyositis Emery-Dreifuss muscular dystrophy lung adenocarcinoma malignant glioma mucopolysaccharidosis type 4 pilocytic astrocytoma Becker muscular dystrophy dry eye syndrome glioblastoma juvenile dermatomyositis lung cancer medulloblastoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth E]	ABA	Parent Component: ALA RESID: AA0253 , AA0409 PSI-MOD : S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819
D [auth E]	BMT	Parent Component: THR RESID: AA0253 , AA0409
D [auth E]	DAL	RESID: AA0253 , AA0409 , AA0111 , AA0191 PSI-MOD : S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819 , meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862
D [auth E]	MLE	Parent Component: LEU RESID: AA0253 , AA0409 , AA0111 , AA0191 , AA0337 PSI-MOD : S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819 , meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , N-methyl-L-leucine MOD:00342
D [auth E]	MVA	Parent Component: VAL RESID: AA0253 , AA0409 , AA0111 , AA0191 , AA0337
D [auth E]	SAR	Parent Component: GLY RESID: AA0253 , AA0409 , AA0111 , AA0191 , AA0337 , AA0063 PSI-MOD : S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819 , meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , N-methyl-L-leucine MOD:00342 , N-methylglycine MOD:00072

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.