2Z1D

Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus kodakaraensis

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	HypD_2nd	e2z1dA3	A: a/b three-layered sandwiches	X: Hydrogenase expression/formation protein HypD (From Topology)	H: Hydrogenase expression/formation protein HypD (From Topology)	T: Hydrogenase expression/formation protein HypD	F: HypD_2nd	ECOD (1.6)
A	HypD_1st	e2z1dA1	A: a/b three-layered sandwiches	X: Hydrogenase expression/formation protein HypD (From Topology)	H: Hydrogenase expression/formation protein HypD (From Topology)	T: Hydrogenase expression/formation protein HypD	F: HypD_1st	ECOD (1.6)
A	HypD_3rd	e2z1dA2	A: few secondary structure elements	X: HypD Fe-S cluster binding domain (From Topology)	H: HypD Fe-S cluster binding domain (From Topology)	T: HypD Fe-S cluster binding domain	F: HypD_3rd	ECOD (1.6)
B	HypD_2nd	e2z1dB3	A: a/b three-layered sandwiches	X: Hydrogenase expression/formation protein HypD (From Topology)	H: Hydrogenase expression/formation protein HypD (From Topology)	T: Hydrogenase expression/formation protein HypD	F: HypD_2nd	ECOD (1.6)
B	HypD_1st	e2z1dB1	A: a/b three-layered sandwiches	X: Hydrogenase expression/formation protein HypD (From Topology)	H: Hydrogenase expression/formation protein HypD (From Topology)	T: Hydrogenase expression/formation protein HypD	F: HypD_1st	ECOD (1.6)
B	HypD_3rd	e2z1dB2	A: few secondary structure elements	X: HypD Fe-S cluster binding domain (From Topology)	H: HypD Fe-S cluster binding domain (From Topology)	T: HypD Fe-S cluster binding domain	F: HypD_3rd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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
A, 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	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002780	Hydrogenase formation HypD protein	Family
A, B	IPR042243	HypD, domain 1	Homologous Superfamily
A, B	IPR042244	HypD, domain 2	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.