5YXY | pdb_00005yxy

Crystal structure of the HyhL-HypA complex (form I)

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	HypA-like	8057059	3002385	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HypA-like	8057059	3002385	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HypA-like	8057059	3002385	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)
F	Chlorophyllase2	e5yxyF1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
E	bZIP_1	e5yxyE1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: bZIP_1	ECOD (v294.1)
D	Chlorophyllase2	e5yxyD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
C	Chlorophyllase2	e5yxyC2	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
B	Chlorophyllase2	e5yxyB2	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.2320.50	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold		CATH (4.3.0)
E	3.30.2320.50	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold		CATH (4.3.0)
D	3.30.2320.50	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E, F	Probable hydrogenase nickel incorporation protein HypA	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding zinc 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, B, C	Cytosolic NiFe-hydrogenase, alpha subunit	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E, F	IPR020538	Hydrogenase nickel incorporation protein HypA/HybF, conserved site	Conserved Site
D, E, F	IPR000688	Hydrogenase maturation factor HypA/HybF	Family
A, B, C	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
A, B, C	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
A, B, C	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
A, B, C	IPR054945	NADPH-dependent hydrogenase/sulfhydrogenase 1 subunit alpha	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.