3VB9 | pdb_00003vb9

Crystal structure of VPA0735 from Vibrio parahaemolyticus in monoclinic form, NorthEast Structural Genomics target VpR109

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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)
D	d3vb9d_	Multi-domain proteins (alpha and beta)	VPA0735-like	VPA0735-like	VPA0735-like	Hypothetical protein VPA0735	(Vibrio parahaemolyticus ) [TaxId: 670 ],	SCOPe (2.08)
C	d3vb9c_	Multi-domain proteins (alpha and beta)	VPA0735-like	VPA0735-like	VPA0735-like	Hypothetical protein VPA0735	(Vibrio parahaemolyticus ) [TaxId: 670 ],	SCOPe (2.08)
B	d3vb9b_	Multi-domain proteins (alpha and beta)	VPA0735-like	VPA0735-like	VPA0735-like	Hypothetical protein VPA0735	(Vibrio parahaemolyticus ) [TaxId: 670 ],	SCOPe (2.08)
A	d3vb9a_	Multi-domain proteins (alpha and beta)	VPA0735-like	VPA0735-like	VPA0735-like	Hypothetical protein VPA0735	(Vibrio parahaemolyticus ) [TaxId: 670 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	VPA0735 beta-sandwich domain-like	8035342	3001579	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	VPA0735 beta-sandwich domain-like	8054389	3001579	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	VPA0735 beta-sandwich domain-like	8054389	3001579	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	VPA0735 beta-sandwich domain-like	8035342	3001579	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	VPA0735 beta-sandwich domain-like	8054389	3001579	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	VPA0735 beta-sandwich domain-like	8035342	3001579	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	VPA0735 beta-sandwich domain-like	8035342	3001579	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	VPA0735 beta-sandwich domain-like	8054389	3001579	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)
D	DUF1214	e3vb9D3	A: beta sandwiches	X: jelly-roll	H: VPA0735-like (From Topology)	T: VPA0735-like	F: DUF1214	ECOD (1.6)
D	DUF1254	e3vb9D4	A: beta sandwiches	X: jelly-roll	H: VPA0735-like (From Topology)	T: VPA0735-like	F: DUF1254	ECOD (1.6)
C	DUF1214	e3vb9C3	A: beta sandwiches	X: jelly-roll	H: VPA0735-like (From Topology)	T: VPA0735-like	F: DUF1214	ECOD (1.6)
C	DUF1254	e3vb9C4	A: beta sandwiches	X: jelly-roll	H: VPA0735-like (From Topology)	T: VPA0735-like	F: DUF1254	ECOD (1.6)
B	DUF1214	e3vb9B3	A: beta sandwiches	X: jelly-roll	H: VPA0735-like (From Topology)	T: VPA0735-like	F: DUF1214	ECOD (1.6)
B	DUF1254	e3vb9B4	A: beta sandwiches	X: jelly-roll	H: VPA0735-like (From Topology)	T: VPA0735-like	F: DUF1254	ECOD (1.6)
A	DUF1214	e3vb9A2	A: beta sandwiches	X: jelly-roll	H: VPA0735-like (From Topology)	T: VPA0735-like	F: DUF1214	ECOD (1.6)
A	DUF1254	e3vb9A1	A: beta sandwiches	X: jelly-roll	H: VPA0735-like (From Topology)	T: VPA0735-like	F: DUF1254	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
D	1.10.3360.10	Mainly Alpha	Orthogonal Bundle	VPA0735-like fold	VPA0735-like domain	CATH (4.3.0)
D	2.60.40.1610	Mainly Beta	Sandwich	Immunoglobulin-like	Domain of unknown function DUF1254	CATH (4.3.0)
D	2.60.120.600	Mainly Beta	Sandwich	Jelly Rolls	Domain of unknown function DUF1214, C-terminal domain	CATH (4.3.0)
C	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
C	1.10.3360.10	Mainly Alpha	Orthogonal Bundle	VPA0735-like fold	VPA0735-like domain	CATH (4.3.0)
C	2.60.40.1610	Mainly Beta	Sandwich	Immunoglobulin-like	Domain of unknown function DUF1254	CATH (4.3.0)
C	2.60.120.600	Mainly Beta	Sandwich	Jelly Rolls	Domain of unknown function DUF1214, C-terminal domain	CATH (4.3.0)
B	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
B	1.10.3360.10	Mainly Alpha	Orthogonal Bundle	VPA0735-like fold	VPA0735-like domain	CATH (4.3.0)
B	2.60.40.1610	Mainly Beta	Sandwich	Immunoglobulin-like	Domain of unknown function DUF1254	CATH (4.3.0)
B	2.60.120.600	Mainly Beta	Sandwich	Jelly Rolls	Domain of unknown function DUF1214, C-terminal domain	CATH (4.3.0)
A	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
A	1.10.3360.10	Mainly Alpha	Orthogonal Bundle	VPA0735-like fold	VPA0735-like domain	CATH (4.3.0)
A	2.60.40.1610	Mainly Beta	Sandwich	Immunoglobulin-like	Domain of unknown function DUF1254	CATH (4.3.0)
A	2.60.120.600	Mainly Beta	Sandwich	Jelly Rolls	Domain of unknown function DUF1214, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF06742	Protein of unknown function (DUF1214) (DUF1214)	Protein of unknown function (DUF1214)	This family represents the C-terminal region of several hypothetical proteins of unknown function. Family members are mostly bacterial, but a few are also found in eukaryotes and archaea.	Domain
A, B, C, D	PF06863	Protein of unknown function (DUF1254) (DUF1254)	Protein of unknown function (DUF1254)	This family represents a conserved region about 130 residues long within hypothetical proteins of unknown function. Family members include eukaryotic, bacterial and archaeal proteins.	Domain

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR010679	Domain of unknown function DUF1254	Domain
A, B, C, D	IPR037050	Domain of unknown function DUF1254 superfamily	Homologous Superfamily
A, B, C, D	IPR037049	Domain of unknown function DUF1214, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR010621	Domain of unknown function DUF1214	Domain

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.