3VYR | pdb_00003vyr

Crystal structure of the HypC-HypD complex

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3vyra_	All beta proteins	OB-fold	HupF/HypC-like	HupF/HypC-like	Hydrogenase expression/formation protein HypC	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8038052	3000354	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		e3vyrB1	A: Restriction endonuclease-like	X: beta-propeller	H: HypD Fe-S cluster binding domain	T: HypD	F:	ECOD (20:10:01)
A		e3vyrA1	A: Globin-like	X: Globin-like	H: Globin-like	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.11750	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HypD, alpha/beta domain 1	CATH (4.3.0)
B	3.40.50.11740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HypD, alpha/beta domain 2	CATH (4.3.0)
B	6.10.20.100	Special	Helix non-globular	Arc Repressor Mutant, subunit A		CATH (4.3.0)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF01924	Hydrogenase formation hypA family (HypD)	Hydrogenase formation hypA family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Hydrogenase expression/formation protein HypD	binding carbon monoxide binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation	-
A	Hydrogenase expression/formation protein HypC	binding carbon dioxide binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR002780	Hydrogenase formation HypD protein	Family
B	IPR042243	HypD, domain 1	Homologous Superfamily
B	IPR042244	HypD, domain 2	Homologous Superfamily
A	IPR019812	Hydrogenase assembly chaperone, conserved site	Conserved Site
A	IPR001109	Hydrogenase expression/formation protein, HupF/HypC	Family

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.