2K9F | pdb_00002k9f

Structural features of the complex between the DsbD N-terminal and the PilB N-terminal domains from Neisseria meningitidis

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	d2k9fa_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Peptide methionine sulfoxide reductase MsrA/MsrB, N-terminal domain	(Neisseria meningitidis serogroup A ) [TaxId: 65699 ],	SCOPe (2.08)
B	d2k9fb1	All beta proteins	Immunoglobulin-like beta-sandwich	Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)	Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)	Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
B	d2k9fb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thioredoxin-like	8057701	3000031	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)	8080437	3002068	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	AhpC-TSA_4	e2k9fA1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_4	ECOD (1.6)
B	DsbC	e2k9fB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: DsbC	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.2.0)
B	2.60.40.1250	Mainly Beta	Sandwich	Immunoglobulin-like	Thiol:disulfide interchange protein DsbD, N-terminal domain	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08534	Redoxin (Redoxin)	Redoxin	This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins.	Domain
B	PF11412	Thiol:disulfide interchange protein DsbD, N-terminal (DsbD_N)	Thiol:disulfide interchange protein DsbD, N-terminal	This entry represents the N-terminal domain of DsbD, a transmembrane electron transporter [1-3]. DsbD binds to a DsbC dimer and selectively activates it using electrons from the cytoplasm. The N-terminal domain of DsbD (DsbDN) is capable of forming d ...	This entry represents the N-terminal domain of DsbD, a transmembrane electron transporter [1-3]. DsbD binds to a DsbC dimer and selectively activates it using electrons from the cytoplasm. The N-terminal domain of DsbD (DsbDN) is capable of forming disulfides with oxidized DsbC, DsbE, or DsbG as well as with reduced DsbD [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Thioredoxin	oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor catalytic activity, acting on a protein catalytic activity peptide-methionine (R)-S-oxide reductase activity peptide-methionine (S)-S-oxide reductase activity	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress	cellular anatomical structure intracellular anatomical structure cytoplasm
B	Thiol:disulfide interchange protein dsbD	oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity catalytic activity protein-disulfide reductase [NAD(P)H] activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor electron transfer activity	cell redox homeostasis cellular homeostasis homeostatic process cytochrome complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002569	Peptide methionine sulphoxide reductase MsrA domain	Domain
A	IPR036509	Peptide methionine sulphoxide reductase MsrA superfamily	Homologous Superfamily
A	IPR013766	Thioredoxin domain	Domain
A	IPR011057	Mss4-like superfamily	Homologous Superfamily
A	IPR050162	Methionine Sulfoxide Reductase A	Family
A	IPR013740	Redoxin	Domain
A	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A	IPR002579	Peptide methionine sulphoxide reductase MrsB domain	Domain
B	IPR028250	Thiol:disulfide interchange protein DsbD, N-terminal domain	Domain
B	IPR013766	Thioredoxin domain	Domain
B	IPR003834	Cytochrome C biogenesis protein, transmembrane domain	Domain
B	IPR012336	Thioredoxin-like fold	Domain
B	IPR022910	Thiol:disulphide interchange protein DsbD	Family
B	IPR035671	DsbD gamma	Domain
B	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
B	IPR036929	Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily	Homologous Superfamily

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.