2YQ8 | pdb_00002yq8

Crystal structure of the SeMet-labeled N-terminal domain and peptide substrate binding domain of alpha subunit of prolyl-4 hydroxylase type I from human.

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	TPR-like	8042488	3001345	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TPR-like	8042488	3001345	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)
B	TPR_2, TPR_P4H	e2yq8B1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: ARM repeat	T: ARM repeat	F: TPR_2, TPR_P4H	ECOD (v294.1)
A	TPR_2, TPR_P4H	e2yq8A1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: ARM repeat	T: ARM repeat	F: TPR_2, TPR_P4H	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	6.10.140.1460	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
A	6.10.140.1460	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08336	Prolyl 4-Hydroxylase alpha-subunit, N-terminal region (P4Ha_N)	Prolyl 4-Hydroxylase alpha-subunit, N-terminal region	-	Family
A, B	PF23558	Prolyl 4-hydroxylase peptide-substrate-binding domain (TPR_P4H)	Prolyl 4-hydroxylase peptide-substrate-binding domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1	cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding organic acid binding carbohydrate binding vitamin binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding organic acid binding carbohydrate binding vitamin binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding peptidyl-proline 4-dioxygenase activity oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen procollagen-proline dioxygenase activity peptidyl-proline dioxygenase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity procollagen-proline 4-dioxygenase activity dioxygenase activity identical protein binding protein binding	cellular component organization collagen fibril organization extracellular matrix organization cellular process cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane protein-containing complex catalytic complex endomembrane system endoplasmic reticulum procollagen-proline 4-dioxygenase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane protein-containing complex catalytic complex endomembrane system endoplasmic reticulum procollagen-proline 4-dioxygenase complex oxidoreductase complex endoplasmic reticulum protein-containing complex membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A, B	IPR044862	Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain	Domain
A, B	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A, B	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A, B	IPR013547	Prolyl 4-hydroxylase, N-terminal	Domain
A, B	IPR045054	Prolyl 4-hydroxylase	Family
A, B	IPR059068	Prolyl 4-hydroxylase, peptide-substrate-binding domain	Domain
A, B	IPR019734	Tetratricopeptide repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P13674	astrocytic tumor Ehlers-Danlos syndrome, musculocontractural type 1 malignant ependymoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma psoriasis atypical teratoid rhabdoid tumor glioblastoma malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ductal breast carcinoma in situ heart disease malignant pancreatic neoplasm ovarian cancer astrocytic tumor Ehlers-Danlos syndrome, musculocontractural type 1 malignant ependymoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma psoriasis atypical teratoid rhabdoid tumor glioblastoma malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ductal breast carcinoma in situ heart disease malignant pancreatic neoplasm ovarian cancer plasma cell myeloma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.