3VYU | pdb_00003vyu

Crystal structure of the HypC-HypD-HypE complex (form II)

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)
C	d3vyuc1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	PurM N-terminal domain-like	PurM N-terminal domain-like	Hydrogenase expression/formation protein HypE	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
C	d3vyuc2	Alpha and beta proteins (a+b)	PurM C-terminal domain-like	PurM C-terminal domain-like	PurM C-terminal domain-like	Hydrogenase expression/formation protein HypE	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
A	d3vyua_	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)
C	SCOP2B Superfamily	PurM C-terminal domain-like	8038061	3000696	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PurM N-terminal domain-like	8038057	3001759	SCOP2B (2022-06-29)
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)
C		e3vyuC3	A: POZ domain	X: POZ domain	H: POZ domain	T:	F:	ECOD (20:10:01)
B		e3vyuB1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: CagX	F:	ECOD (20:10:01)
A		e3vyuA1	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)
C	3.30.1330.10	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.90.650.10	Alpha Beta	Alpha-Beta Complex	Phosphoribosyl-aminoimidazole Synthetase	Chain A, domain 2	CATH (4.3.0)
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
C	PF02769	AIR synthase related protein, C-terminal domain (AIRS_C)	AIR synthase related protein, C-terminal domain	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of ...	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site [1].	Domain
C	PF00586	AIR synthase related protein, N-terminal domain (AIRS)	AIR synthase related protein, N-terminal domain	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase fo ...	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain [1].	Domain
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
C	Hydrogenase expression/formation protein HypE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation 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	-
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
C	IPR036676	PurM-like, C-terminal domain superfamily	Homologous Superfamily
C	IPR010918	PurM-like, C-terminal domain	Domain
C	IPR016188	PurM-like, N-terminal domain	Domain
C	IPR036921	PurM-like, N-terminal domain superfamily	Homologous Superfamily
C	IPR011854	Carbamoyl dehydratase HypE	Family
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.