6QGY

Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6qgyb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d6qgyd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Outer-membrane protein Omp85-like	8098379	4006144	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Porins	8098380	3000224	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)
A	Bac_surface_Ag	e6qgyA1	A: beta barrels	X: Outer membrane meander beta-barrels	H: Porins	T: Porin	F: Bac_surface_Ag	ECOD (1.6)
C	Bac_surface_Ag	e6qgyC1	A: beta barrels	X: Outer membrane meander beta-barrels	H: Porins	T: Porin	F: Bac_surface_Ag	ECOD (1.6)
B	V-set_12	e6qgyB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
D	V-set_12	e6qgyD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.160.50	Mainly Beta	Beta Barrel	Porin	membrane protein fhac: a member of the omp85/tpsb transporter family	CATH (utative)
C	2.40.160.50	Mainly Beta	Beta Barrel	Porin	membrane protein fhac: a member of the omp85/tpsb transporter family	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Heavy Chain	IGHV1	-	outer membrane protein assembly factor bama	SAbDab (2024-12-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF01103	Omp85 superfamily domain (Omp85)	Omp85 superfamily domain	The Omp85 protein superfamily contains bacterial outer membrane proteins, which can function as protein translocases or as membrane protein assembly factors [1]. The family includes the membrane bound beta barrel of proteins such as BamA and TamA fro ...	The Omp85 protein superfamily contains bacterial outer membrane proteins, which can function as protein translocases or as membrane protein assembly factors [1]. The family includes the membrane bound beta barrel of proteins such as BamA and TamA from E. coli.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Outer membrane protein assembly factor BamA	-	membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization protein localization cellular localization establishment of protein localization membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization protein localization cellular localization establishment of protein localization establishment of protein localization to membrane localization within membrane protein localization to membrane establishment of localization localization cellular macromolecule localization macromolecule localization protein insertion into membrane cell adhesion	cellular anatomical structure membrane cell periphery cell outer membrane external encapsulating structure cell envelope outer membrane protein-containing complex periplasmic side of cell outer membrane membrane protein complex side of membrane Bam protein complex
B, D	NanoB12	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR039910	Surface antigen D15-like	Family
A, C	IPR034746	POTRA domain	Domain
A, C	IPR000184	Bacterial surface antigen (D15)	Domain
A, C	IPR010827	POTRA domain, BamA/TamA-like	Domain
A, C	IPR023707	Outer membrane protein assembly factor BamA	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, C	OPM	Transmembrane	Beta-barrel transmembrane	Omp85-TpsB transporters (n=16,S=20,22)	OMP insertion (Bam complex) porin (n=16,S=22)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, C	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Omp85-TpsB Outer Membrane Transporter Superfamily	BamA in complex with nanobody E6

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.