5WAQ | pdb_00005waq

Structure of BamD from Neisseria gonorrhoeae

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Outer membrane lipoprotein-like	8061315	4006249	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TPR-like	8061316	3001345	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		e5waqA1	A: Cryptochrome/photolyase FAD-binding domain-related	X: Cryptochrome/photolyase FAD-binding domain-related	H: Undecaprenyl diphosphate synthase	T: RuBisCO_large_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13525	Outer membrane lipoprotein (YfiO)	Outer membrane lipoprotein	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Outer membrane protein assembly factor BamD	-	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 establishment of protein localization cellular localization establishment of protein localization to membrane 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 establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane establishment of localization localization macromolecule localization intracellular protein localization protein insertion into membrane DNA-mediated transformation cellular response to stimulus horizontal gene transfer response to stimulus establishment of competence for transformation	protein-containing complex membrane periplasmic side of cell outer membrane membrane protein complex side of membrane Bam protein complex cell periphery cell outer membrane cellular anatomical structure external encapsulating structure cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR039565	Outer membrane lipoprotein BamD-like	Domain
A	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A	IPR017689	Outer membrane protein assembly factor BamD	Family

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Omp85-TpsB Outer Membrane Transporter Superfamily	BamD component of the Bam β-barrel assembly machine

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.