SMTL ID : 5onu.1

Trimeric OmpU structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-trimer

Ligands

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

C8E.1: 9 residues within 4Å: Chain A: I.33, R.250, E.252, N.253, G.279, Y.280, K.281, T.288, Y.312 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.33, A:T.288 Hydrogen bonds: A:K.281 C8E.7: 12 residues within 4Å: Chain B: G.32, I.33, R.250, E.252, N.253, G.279, Y.280, K.281, G.283, Q.284, T.288, Y.312 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.33, B:T.288 Hydrogen bonds: B:K.281, B:Q.284 C8E.14: 12 residues within 4Å: Chain C: G.32, I.33, Q.35, R.250, E.252, N.253, G.279, Y.280, K.281, A.286, T.288, Y.312 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Q.35, C:A.286, C:T.288 Hydrogen bonds: C:K.281

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: S.36, R.74, R.76, R.116 Ligands: GOL.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.74, A:R.74, A:R.76, A:R.76, A:R.116 Water bridges: A:D.38, A:D.38, A:R.61 GOL.3: 4 residues within 4Å: Chain A: R.116, D.163, R.164 Ligands: GOL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.116, A:R.116, A:D.163, A:R.164 Water bridges: A:N.153, A:K.158 GOL.8: 5 residues within 4Å: Chain B: S.36, G.37, R.74, R.76 Ligands: GOL.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.36, B:S.36, B:R.74, B:R.74, B:R.76, B:R.76 Water bridges: B:D.38, B:D.38, B:R.61 GOL.9: 5 residues within 4Å: Chain B: R.116, D.163, R.164 Chain C: N.107 Ligands: GOL.8 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:N.107, B:R.116, B:R.116, B:D.163, B:R.164, B:R.164 Water bridges: B:D.163 GOL.15: 5 residues within 4Å: Chain C: S.36, R.74, R.76, R.116 Ligands: GOL.16 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.36, C:R.74, C:R.74, C:R.76, C:R.76, C:R.116 Water bridges: C:S.36, C:D.38, C:D.38, C:R.61, C:Y.150 GOL.16: 5 residues within 4Å: Chain A: N.107 Chain C: R.116, D.163, R.164 Ligands: GOL.15 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.116, C:R.116, C:D.163, C:R.164, C:R.164, A:N.107 Water bridges: C:K.158, C:K.158

10 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.4: 4 residues within 4Å: Chain A: Y.274, N.293, E.295, K.298 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.274, A:Y.274 Salt bridges: A:E.295 LDA.5: 5 residues within 4Å: Chain A: Y.280, F.287, T.288, I.307, D.308 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.287, A:F.287, A:I.307 LDA.6: 6 residues within 4Å: Chain A: A.285, A.309, Y.311, S.319, I.321, I.344 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.285, A:A.309, A:Y.311, A:Y.311, A:I.321, A:I.344 LDA.10: 6 residues within 4Å: Chain B: Y.274, Y.291, N.293, E.295, K.298, T.300 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.274, B:Y.274, B:Y.274, B:Y.291 Salt bridges: B:E.295 LDA.11: 4 residues within 4Å: Chain B: F.287, T.288, A.289, D.308 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.287, B:A.289 pi-Cation interactions: B:F.287 LDA.12: 1 residues within 4Å: Chain B: F.305 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.305 LDA.13: 4 residues within 4Å: Chain B: Y.221, V.230, G.231, A.232 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.221, B:V.230 LDA.17: 4 residues within 4Å: Chain C: L.178, A.219, Y.221, V.230 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.219, C:V.230 LDA.18: 4 residues within 4Å: Chain C: F.175, G.176, D.177, Y.221 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.221 Salt bridges: C:D.177 LDA.19: 7 residues within 4Å: Chain B: I.122 Chain C: A.309, Y.311, S.319, Y.320, I.321, I.344 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.309, C:Y.311, C:I.321, C:I.344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Crystal structure of the outer membrane protein OmpU from Vibrio cholerae at 2.2 angstrom resolution. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-01-03

Peptides

Outer membrane protein OmpU: 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 OmpU