4R40 | pdb_00004r40

Crystal Structure of TolB/Pal complex from Yersinia pestis.

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)
D	d4r40d_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	OmpA-like	OmpA-like	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)
B	d4r40b_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	OmpA-like	OmpA-like	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)
C	d4r40c2	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)
C	d4r40c1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	automated matches	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)
A	d4r40a2	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)
A	d4r40a1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	automated matches	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	OmpA-like	8074164	4001470	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	OmpA-like	8074165	3001650	SCOP2 (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	V-set	e4r40D1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
B	V-set	e4r40B1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
C	V-set	e4r40C1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
A	V-set	e4r40A1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.1330.60	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.30.1330.60	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.40.50.10070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TolB, N-terminal domain	CATH (4.3.0)
C	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)
A	3.40.50.10070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TolB, N-terminal domain	CATH (4.3.0)
A	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00691	OmpA family (OmpA)	OmpA family	-	Family
A, C	PF04052	TolB amino-terminal domain (TolB_N)	TolB amino-terminal domain	TolB is an essential periplasmic component of the tol-dependent translocation system. This function of this amino terminal domain is uncertain.	Domain
A, C	PF07676	WD40-like Beta Propeller Repeat (PD40)	WD40-like Beta Propeller Repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Peptidoglycan-associated lipoprotein	-	cellular process cell division	cell outer membrane cellular anatomical structure external encapsulating structure extracellular region membrane cell envelope outer membrane
A, C	Protein TolB	-	cell septum assembly cytokinesis cellular component biogenesis cellular component organization cellular component assembly cytokinetic process cellular process cell cycle cell division cellular component organization or biogenesis cell cycle process protein import localization establishment of protein localization cell septum assembly cytokinesis cellular component biogenesis cellular component organization cellular component assembly cytokinetic process cellular process cell cycle cell division cellular component organization or biogenesis cell cycle process protein import localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization	cellular anatomical structure extracellular region periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR006664	Outer membrane protein, bacterial	Domain
B, D	IPR006665	OmpA-like domain	Domain
B, D	IPR039001	Peptidoglycan-associated lipoprotein	Family
B, D	IPR006690	Outer membrane protein, OmpA-like, conserved site	Conserved Site
B, D	IPR014169	Peptidoglycan-associated lipoprotein, C-terminal	Domain
B, D	IPR050330	Bacterial Outer Membrane Structural/Functional	Family
B, D	IPR036737	OmpA-like domain superfamily	Homologous Superfamily
A, C	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A, C	IPR011659	WD40-like beta-propeller	Repeat
A, C	IPR007195	TolB, N-terminal	Domain
A, C	IPR014167	Tol-Pal system protein TolB	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.