3TD5 | pdb_00003td5

Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	OmpA-like	8075232	3001650	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	OmpA-like	8075232	3001650	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	OmpA-like	8075232	3001650	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	OmpA-like	8075232	3001650	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	OmpA-like	8075232	3001650	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	OmpA-like	8075232	3001650	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	OmpA-like	8075232	3001650	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	OmpA-like	8075232	3001650	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)
A	Binary_toxB	e3td5A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Binary_toxB	ECOD (v294.1)
H	Binary_toxB	e3td5H1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Binary_toxB	ECOD (v294.1)
G	Binary_toxB	e3td5G1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Binary_toxB	ECOD (v294.1)
F	Binary_toxB	e3td5F1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Binary_toxB	ECOD (v294.1)
E	Binary_toxB	e3td5E1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Binary_toxB	ECOD (v294.1)
D	Binary_toxB	e3td5D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Binary_toxB	ECOD (v294.1)
C	Binary_toxB	e3td5C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Binary_toxB	ECOD (v294.1)
B	Binary_toxB	e3td5B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Binary_toxB	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1330.60	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
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)
F	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)
D	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)
B	3.30.1330.60	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00691	OmpA family (OmpA)	OmpA family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J, K, L, M I, J, K, L, M, N, O, P	peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)	-	-	-
A, B, C, D, E A, B, C, D, E, F, G, H	Outer membrane protein omp38	wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity	localization transport monoatomic ion transport establishment of localization	protein-containing complex cellular anatomical structure membrane pore complex membrane protein complex cell outer membrane external encapsulating structure extracellular region cell envelope outer membrane host intracellular membrane-bounded organelle host cellular component host intracellular part other organism part protein-containing complex cellular anatomical structure membrane pore complex membrane protein complex cell outer membrane external encapsulating structure extracellular region cell envelope outer membrane host intracellular membrane-bounded organelle host cellular component host intracellular part other organism part host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR054882	Outer membrane protein Omp38	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006664	Outer membrane protein, bacterial	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006665	OmpA-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050330	Bacterial Outer Membrane Structural/Functional	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR027385	Outer membrane protein, beta-barrel domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036737	OmpA-like domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
I, J, K, L, M I, J, K, L, M, N, O, P	API	Parent Component: LYS
I, J, K, L, M I, J, K, L, M, N, O, P	DAL	RESID: AA0111 , AA0191 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862
I, J, K, L, M I, J, K, L, M, N, O, P	FGA	RESID: AA0111 , AA0191

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.