SMTL ID : 6ehb.1

OmpU, an outer membrane protein, of Vibrio cholerae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-trimer

Ligands

23 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.1: 6 residues within 4Å: Chain A: A.30, L.32, I.314, G.315, L.316 Chain C: Y.101 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:Y.101, C:Y.101, A:A.30, A:L.32, A:L.32, A:I.314, A:L.316 C8E.2: 2 residues within 4Å: Chain A: Y.191, F.193 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.191, A:Y.191, A:F.193 C8E.3: 3 residues within 4Å: Chain A: F.193, T.196, F.198 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.193, A:F.193, A:T.196, A:F.198, A:F.198 C8E.4: 5 residues within 4Å: Chain A: A.279, Y.281, S.289, Y.290, I.291 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.281, A:I.291 C8E.5: 2 residues within 4Å: Chain A: G.203, Y.204 No protein-ligand interaction detected (PLIP) C8E.6: 7 residues within 4Å: Chain A: V.200, G.201, L.215, A.216, A.217, G.228, L.229 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.217 C8E.7: 2 residues within 4Å: Chain A: T.196, F.198 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.196 C8E.8: 6 residues within 4Å: Chain A: Y.101 Chain B: A.30, L.32, I.314, G.315, L.316 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.101, A:Y.101, B:A.30, B:L.32, B:I.314, B:L.316 C8E.9: 3 residues within 4Å: Chain B: F.64, Y.87, Y.89 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.64, B:Y.87 C8E.10: 5 residues within 4Å: Chain B: G.2, I.3, R.220, K.251, Y.282 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.251 C8E.11: 8 residues within 4Å: Chain B: L.246, A.247, A.248, A.259, Y.261, F.275 Ligands: C8E.12, C8E.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.275 C8E.12: 3 residues within 4Å: Chain B: Y.244 Ligands: C8E.11, C8E.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.244 C8E.13: 4 residues within 4Å: Chain B: Y.261, D.273 Ligands: C8E.11, C8E.12 No protein-ligand interaction detected (PLIP) C8E.14: 5 residues within 4Å: Chain B: A.279, Y.281, S.289, Y.290, I.291 No protein-ligand interaction detected (PLIP) C8E.15: 4 residues within 4Å: Chain C: G.2, I.3, K.251, Y.282 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.282, C:Y.282 C8E.16: 10 residues within 4Å: Chain C: I.3, Q.5, R.220, N.223, L.224, Y.225, G.249, Y.250, K.251, T.258 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.225 Hydrogen bonds: C:I.3 C8E.17: 5 residues within 4Å: Chain C: L.59, I.92, Y.96, G.97, Y.141 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.59, C:Y.141 C8E.18: 10 residues within 4Å: Chain B: Y.101, L.139, F.156 Chain C: A.30, L.32, L.34, G.37, I.314, G.315, L.316 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:Y.101, B:L.139, B:L.139, C:A.30, C:I.314, C:L.316 C8E.19: 1 residues within 4Å: Ligands: C8E.20 No protein-ligand interaction detected (PLIP) C8E.20: 5 residues within 4Å: Chain C: A.189, V.200, A.202, L.215 Ligands: C8E.19 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.200, C:A.202, C:L.215 C8E.21: 5 residues within 4Å: Chain C: L.246, A.247, A.248, A.259, Y.261 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.261 C8E.22: 5 residues within 4Å: Chain C: L.224, A.248, F.257, T.258, D.278 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.224, C:F.257 C8E.23: 7 residues within 4Å: Chain C: A.255, A.279, Y.281, S.289, Y.290, I.291, I.314 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pathania, M. et al., Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae. Structure (2018)

Release Date

2018-04-25

Peptides

Outer membrane protein U: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Outer membrane protein U