2W8B | pdb_00002w8b

Crystal structure of processed TolB in complex with Pal

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)
H	d2w8bh1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	OmpA-like	OmpA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d2w8bh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d2w8bg1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	OmpA-like	OmpA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d2w8bg2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2w8be1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	OmpA-like	OmpA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2w8be2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2w8bc_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	OmpA-like	OmpA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2w8bf2	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2w8bf1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2w8bd2	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2w8bd1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2w8bb2	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2w8bb1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2w8ba2	All beta proteins	6-bladed beta-propeller	TolB, C-terminal domain	TolB, C-terminal domain	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2w8ba1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	TolB, N-terminal domain	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	OmpA-like	8042389	3001650	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	OmpA-like	8042389	3001650	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	OmpA-like	8042389	3001650	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	OmpA-like	8042389	3001650	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TolB N-terminal domain-like	8042388	3000482	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YWTD domain-like	8042387	3000494	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YWTD domain-like	8042387	3000494	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TolB N-terminal domain-like	8042388	3000482	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YWTD domain-like	8042387	3000494	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TolB N-terminal domain-like	8042388	3000482	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TolB N-terminal domain-like	8042388	3000482	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	YWTD domain-like	8042387	3000494	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)
H	OmpA	e2w8bH1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: OmpA-like (From Topology)	T: OmpA-like	F: OmpA	ECOD (1.6)
G	OmpA	e2w8bG1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: OmpA-like (From Topology)	T: OmpA-like	F: OmpA	ECOD (1.6)
E	OmpA	e2w8bE1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: OmpA-like (From Topology)	T: OmpA-like	F: OmpA	ECOD (1.6)
C	OmpA	e2w8bC1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: OmpA-like (From Topology)	T: OmpA-like	F: OmpA	ECOD (1.6)
F	DPPIV_N_1	e2w8bF1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: DPPIV_N_1	ECOD (1.6)
F	TolB_N	e2w8bF2	A: a/b three-layered sandwiches	X: TolB, N-terminal domain (From Topology)	H: TolB, N-terminal domain (From Topology)	T: TolB, N-terminal domain	F: TolB_N	ECOD (1.6)
D	DPPIV_N_1	e2w8bD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: DPPIV_N_1	ECOD (1.6)
D	TolB_N	e2w8bD2	A: a/b three-layered sandwiches	X: TolB, N-terminal domain (From Topology)	H: TolB, N-terminal domain (From Topology)	T: TolB, N-terminal domain	F: TolB_N	ECOD (1.6)
B	DPPIV_N_1	e2w8bB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: DPPIV_N_1	ECOD (1.6)
B	TolB_N	e2w8bB2	A: a/b three-layered sandwiches	X: TolB, N-terminal domain (From Topology)	H: TolB, N-terminal domain (From Topology)	T: TolB, N-terminal domain	F: TolB_N	ECOD (1.6)
A	DPPIV_N_1	e2w8bA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: DPPIV_N_1	ECOD (1.6)
A	TolB_N	e2w8bA2	A: a/b three-layered sandwiches	X: TolB, N-terminal domain (From Topology)	H: TolB, N-terminal domain (From Topology)	T: TolB, N-terminal domain	F: TolB_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.1330.60	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
G	3.30.1330.60	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
E	3.30.1330.60	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.30.1330.60	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
F	3.40.50.10070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TolB, N-terminal domain	CATH (4.3.0)
F	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)
D	3.40.50.10070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TolB, N-terminal domain	CATH (4.3.0)
D	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)
B	3.40.50.10070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TolB, N-terminal domain	CATH (4.3.0)
B	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
C, E, G, H	PF00691	OmpA family (OmpA)	OmpA family	-	Family
B, D, F	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
B, D, F	PF07676	WD40-like Beta Propeller Repeat (PD40)	WD40-like Beta Propeller Repeat	-	Repeat
A	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	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
C, E, G, H	PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN	-	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 membrane organization regulation of biological process regulation of cellular component organization 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 membrane organization regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation membrane invagination regulation of membrane invagination	cellular anatomical structure membrane cell division site cell periphery cell outer membrane external encapsulating structure cell envelope outer membrane
B, D, F	PROTEIN TOLB	protein binding binding protein domain specific binding protein-containing complex binding	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 nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization amide transport bacteriocin transport membrane organization regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation membrane invagination regulation of membrane invagination cellular response to nitrogen compound cellular response to stimulus response to bacteriocin response to stimulus response to oxygen-containing compound response to nitrogen compound response to antibiotic cellular response to oxygen-containing compound cellular response to antibiotic cellular response to chemical stimulus cellular response to bacteriocin response to chemical	cellular anatomical structure membrane cell division site periplasmic space outer membrane-bounded periplasmic space cell envelope protein-containing complex
A	PROTEIN TOLB	protein binding binding protein domain specific binding protein-containing complex binding	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 nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization amide transport bacteriocin transport membrane organization regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation membrane invagination regulation of membrane invagination cellular response to nitrogen compound cellular response to stimulus response to bacteriocin response to stimulus response to oxygen-containing compound response to nitrogen compound response to antibiotic cellular response to oxygen-containing compound cellular response to antibiotic cellular response to chemical stimulus cellular response to bacteriocin response to chemical	cellular anatomical structure membrane cell division site periplasmic space outer membrane-bounded periplasmic space cell envelope protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

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