4YKG

Crystal Structure of the Alkylhydroperoxide Reductase subunit F (AhpF) with NAD+ from Escherichia coli

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thioredoxin reductase-like	8057768	3000050	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)
A	Thioredoxin_3	e4ykgA2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin_3	ECOD (1.6)
A	UNK_F_TYPE	e4ykgA4	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: UNK_F_TYPE	ECOD (1.6)
A	Pyr_redox_2_1	e4ykgA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
A	Pyr_redox_2	e4ykgA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.30.80	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin		CATH (4.3.0)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13192	Thioredoxin domain (Thioredoxin_3)	Thioredoxin domain	-	Domain
A	PF00070	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Alkyl hydroperoxide reductase subunit F	thioredoxin-disulfide reductase (NADPH) activity oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity disulfide oxidoreductase activity antioxidant activity catalytic activity, acting on a protein protein-disulfide reductase activity protein-disulfide reductase (NAD(P)H) activity catalytic activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor alkyl hydroperoxide reductase activity FAD binding flavin adenine dinucleotide binding binding thioredoxin-disulfide reductase (NADPH) activity oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity disulfide oxidoreductase activity antioxidant activity catalytic activity, acting on a protein protein-disulfide reductase activity protein-disulfide reductase (NAD(P)H) activity catalytic activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor alkyl hydroperoxide reductase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding NAD binding purine nucleotide binding adenyl nucleotide binding	catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process cell redox homeostasis cellular homeostasis homeostatic process response to oxidative stress response to stimulus response to stress response to chemical response to oxygen-containing compound catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process cell redox homeostasis cellular homeostasis homeostatic process response to oxidative stress response to stimulus response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species	protein-containing complex cellular anatomical structure intracellular anatomical structure alkyl hydroperoxide reductase complex cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR044142	AhpF, N-terminal domain, N-terminal TRX-fold subdomain	Domain
A	IPR050097	Ferredoxin--NADP reductase type 2	Family
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR044141	AhpF, N-terminal domain, C-terminal TRX-fold subdomain	Domain
A	IPR008255	Pyridine nucleotide-disulphide oxidoreductase, class-II, active site	Active Site
A	IPR012336	Thioredoxin-like fold	Domain
A	IPR012081	Alkyl hydroperoxide reductase subunit F	Family
A	IPR023753	FAD/NAD(P)-binding domain	Domain
A	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily

Protein Modification Annotation

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

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.