3TCF

Crystal structure of E. coli OppA complexed with endogenous ligands


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad3tcfa_ Alpha and beta proteins (a/b) Periplasmic binding protein-like II Periplasmic binding protein-like II Phosphate binding protein-like automated matches (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Bd3tcfb_ Alpha and beta proteins (a/b) Periplasmic binding protein-like II Periplasmic binding protein-like II Phosphate binding protein-like automated matches (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Cd3tcfc_ Alpha and beta proteins (a/b) Periplasmic binding protein-like II Periplasmic binding protein-like II Phosphate binding protein-like automated matches (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Dd3tcfd_ Alpha and beta proteins (a/b) Periplasmic binding protein-like II Periplasmic binding protein-like II Phosphate binding protein-like automated matches (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Ed3tcfe_ Alpha and beta proteins (a/b) Periplasmic binding protein-like II Periplasmic binding protein-like II Phosphate binding protein-like automated matches (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Fd3tcff_ Alpha and beta proteins (a/b) Periplasmic binding protein-like II Periplasmic binding protein-like II Phosphate binding protein-like automated matches (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Gd3tcfg_ Alpha and beta proteins (a/b) Periplasmic binding protein-like II Periplasmic binding protein-like II Phosphate binding protein-like automated matches (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Hd3tcfh_ Alpha and beta proteins (a/b) Periplasmic binding protein-like II Periplasmic binding protein-like II Phosphate binding protein-like automated matches (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilyPhosphate binding protein-like 8072676 4000229 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyType 2 solute binding protein-like 8072677 3000083 SCOP2 (2022-06-29)
BSCOP2B SuperfamilyType 2 solute binding protein-like 8072677 3000083 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyType 2 solute binding protein-like 8072677 3000083 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyType 2 solute binding protein-like 8072677 3000083 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyType 2 solute binding protein-like 8072677 3000083 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyType 2 solute binding protein-like 8072677 3000083 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyType 2 solute binding protein-like 8072677 3000083 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyType 2 solute binding protein-like 8072677 3000083 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ASBP_bac_5_1ste3tcfA3 A: a+b two layersX: Alpha-beta plaitsH: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)T: Oligo-peptide binding protein (OPPA) insertion domainF: SBP_bac_5_1stECOD (1.6)
ASBP_bac_5_3rde3tcfA1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_3rdECOD (1.6)
ASBP_bac_5_2nde3tcfA4 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_2ndECOD (1.6)
BSBP_bac_5_1ste3tcfB3 A: a+b two layersX: Alpha-beta plaitsH: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)T: Oligo-peptide binding protein (OPPA) insertion domainF: SBP_bac_5_1stECOD (1.6)
BSBP_bac_5_3rde3tcfB1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_3rdECOD (1.6)
BSBP_bac_5_2nde3tcfB2 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_2ndECOD (1.6)
CSBP_bac_5_1ste3tcfC3 A: a+b two layersX: Alpha-beta plaitsH: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)T: Oligo-peptide binding protein (OPPA) insertion domainF: SBP_bac_5_1stECOD (1.6)
CSBP_bac_5_3rde3tcfC1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_3rdECOD (1.6)
CSBP_bac_5_2nde3tcfC4 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_2ndECOD (1.6)
DSBP_bac_5_1ste3tcfD3 A: a+b two layersX: Alpha-beta plaitsH: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)T: Oligo-peptide binding protein (OPPA) insertion domainF: SBP_bac_5_1stECOD (1.6)
DSBP_bac_5_3rde3tcfD2 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_3rdECOD (1.6)
DSBP_bac_5_2nde3tcfD4 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_2ndECOD (1.6)
ESBP_bac_5_1ste3tcfE3 A: a+b two layersX: Alpha-beta plaitsH: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)T: Oligo-peptide binding protein (OPPA) insertion domainF: SBP_bac_5_1stECOD (1.6)
ESBP_bac_5_3rde3tcfE2 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_3rdECOD (1.6)
ESBP_bac_5_2nde3tcfE4 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_2ndECOD (1.6)
FSBP_bac_5_1ste3tcfF3 A: a+b two layersX: Alpha-beta plaitsH: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)T: Oligo-peptide binding protein (OPPA) insertion domainF: SBP_bac_5_1stECOD (1.6)
FSBP_bac_5_3rde3tcfF1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_3rdECOD (1.6)
FSBP_bac_5_2nde3tcfF2 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_2ndECOD (1.6)
GSBP_bac_5_1ste3tcfG3 A: a+b two layersX: Alpha-beta plaitsH: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)T: Oligo-peptide binding protein (OPPA) insertion domainF: SBP_bac_5_1stECOD (1.6)
GSBP_bac_5_3rde3tcfG2 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_3rdECOD (1.6)
GSBP_bac_5_2nde3tcfG1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_2ndECOD (1.6)
HSBP_bac_5_1ste3tcfH3 A: a+b two layersX: Alpha-beta plaitsH: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)T: Oligo-peptide binding protein (OPPA) insertion domainF: SBP_bac_5_1stECOD (1.6)
HSBP_bac_5_3rde3tcfH1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_3rdECOD (1.6)
HSBP_bac_5_2nde3tcfH4 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_5_2ndECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.190.10 Alpha Beta 3-Layer(aba) Sandwich D-Maltodextrin-Binding Protein domain 2CATH (4.3.0)
A3.90.76.10 Alpha Beta Alpha-Beta Complex Dipeptide-binding Protein domain 1CATH (4.3.0)
A3.10.105.10 Alpha Beta Roll Dipeptide-binding Protein domain 3CATH (4.3.0)
B3.40.190.10 Alpha Beta 3-Layer(aba) Sandwich D-Maltodextrin-Binding Protein domain 2CATH (4.3.0)
B3.90.76.10 Alpha Beta Alpha-Beta Complex Dipeptide-binding Protein domain 1CATH (4.3.0)
B3.10.105.10 Alpha Beta Roll Dipeptide-binding Protein domain 3CATH (4.3.0)
C3.40.190.10 Alpha Beta 3-Layer(aba) Sandwich D-Maltodextrin-Binding Protein domain 2CATH (4.3.0)
C3.90.76.10 Alpha Beta Alpha-Beta Complex Dipeptide-binding Protein domain 1CATH (4.3.0)
C3.10.105.10 Alpha Beta Roll Dipeptide-binding Protein domain 3CATH (4.3.0)
D3.40.190.10 Alpha Beta 3-Layer(aba) Sandwich D-Maltodextrin-Binding Protein domain 2CATH (4.3.0)
D3.90.76.10 Alpha Beta Alpha-Beta Complex Dipeptide-binding Protein domain 1CATH (4.3.0)
D3.10.105.10 Alpha Beta Roll Dipeptide-binding Protein domain 3CATH (4.3.0)
E3.40.190.10 Alpha Beta 3-Layer(aba) Sandwich D-Maltodextrin-Binding Protein domain 2CATH (4.3.0)
E3.90.76.10 Alpha Beta Alpha-Beta Complex Dipeptide-binding Protein domain 1CATH (4.3.0)
E3.10.105.10 Alpha Beta Roll Dipeptide-binding Protein domain 3CATH (4.3.0)
F3.40.190.10 Alpha Beta 3-Layer(aba) Sandwich D-Maltodextrin-Binding Protein domain 2CATH (4.3.0)
F3.90.76.10 Alpha Beta Alpha-Beta Complex Dipeptide-binding Protein domain 1CATH (4.3.0)
F3.10.105.10 Alpha Beta Roll Dipeptide-binding Protein domain 3CATH (4.3.0)
G3.40.190.10 Alpha Beta 3-Layer(aba) Sandwich D-Maltodextrin-Binding Protein domain 2CATH (4.3.0)
G3.90.76.10 Alpha Beta Alpha-Beta Complex Dipeptide-binding Protein domain 1CATH (4.3.0)
G3.10.105.10 Alpha Beta Roll Dipeptide-binding Protein domain 3CATH (4.3.0)
H3.40.190.10 Alpha Beta 3-Layer(aba) Sandwich D-Maltodextrin-Binding Protein domain 2CATH (4.3.0)
H3.90.76.10 Alpha Beta Alpha-Beta Complex Dipeptide-binding Protein domain 1CATH (4.3.0)
H3.10.105.10 Alpha Beta Roll Dipeptide-binding Protein domain 3CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF00496Bacterial extracellular solute-binding proteins, family 5 Middle (SBP_bac_5)Bacterial extracellular solute-binding proteins, family 5 MiddleThe borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202.Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D, E
Periplasmic oligopeptide-binding protein
I, J, K, L, M
Endogenous peptide---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR030678Peptide/nickel binding protein, MppA-typeFamily
A, B, C, D, E
IPR023765Solute-binding protein family 5, conserved siteConserved Site
A, B, C, D, E
IPR000914Solute-binding protein family 5 domainDomain
A, B, C, D, E
IPR039424Solute-binding protein family 5Family