SMTL ID : 5nsw.1

Xenon for tunnelling analysis of the efflux pump component OprN.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

6 x PLM: PALMITIC ACID(Covalent)

PLM.1: 4 residues within 4Å: Chain A: C.1, L.120, F.121, V.293 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.120, A:V.293 PLM.2: 2 residues within 4Å: Chain A: C.1, L.120 No protein-ligand interaction detected (PLIP) PLM.14: 4 residues within 4Å: Chain B: C.1, L.120, F.121, P.291 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:P.291 PLM.15: 7 residues within 4Å: Chain B: C.1, R.78, F.79, W.116, L.118, L.120, R.125 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.79, B:W.116 PLM.22: 5 residues within 4Å: Chain C: C.1, L.289, F.290, P.291, R.334 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.290, C:F.290 PLM.23: 2 residues within 4Å: Chain C: C.1, L.120 No protein-ligand interaction detected (PLIP)

17 x XE: XENON(Non-covalent)(Non-functional Binders)

XE.3: 7 residues within 4Å: Chain A: L.405, D.409, R.412 Chain B: L.405, D.409 Chain C: L.405, D.409 Ligand excluded by PLIP XE.4: 4 residues within 4Å: Chain A: Q.177, S.180, A.201, E.411 Ligand excluded by PLIP XE.5: 4 residues within 4Å: Chain A: P.213, Q.214 Chain C: K.371, R.372 Ligand excluded by PLIP XE.6: 1 residues within 4Å: Chain A: S.84 Ligand excluded by PLIP XE.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP XE.8: 3 residues within 4Å: Chain A: R.372, R.375 Chain B: Q.214 Ligand excluded by PLIP XE.11: 1 residues within 4Å: Chain B: D.109 Ligand excluded by PLIP XE.12: 1 residues within 4Å: Chain B: A.86 Ligand excluded by PLIP XE.13: 1 residues within 4Å: Chain B: S.84 Ligand excluded by PLIP XE.16: 5 residues within 4Å: Chain B: Q.177, S.180, A.201, R.204, E.411 Ligand excluded by PLIP XE.17: 3 residues within 4Å: Chain B: S.50, L.51, L.149 Ligand excluded by PLIP XE.18: 3 residues within 4Å: Chain B: R.372, R.375 Chain C: Q.214 Ligand excluded by PLIP XE.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP XE.25: 3 residues within 4Å: Chain C: Q.177, A.201, E.411 Ligand excluded by PLIP XE.26: 2 residues within 4Å: Chain C: S.50, L.149 Ligand excluded by PLIP XE.27: 1 residues within 4Å: Chain C: R.225 Ligand excluded by PLIP XE.28: 1 residues within 4Å: Chain C: S.84 Ligand excluded by PLIP

4 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.9: 1 residues within 4Å: Chain A: S.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.307 BOG.19: 7 residues within 4Å: Chain B: V.3, G.4, P.5, T.286, L.289, F.290, K.341 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.286 Hydrogen bonds: B:G.4 Water bridges: B:G.4 BOG.20: 5 residues within 4Å: Chain B: W.325, A.327, F.328, L.330, R.334 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.325, B:A.327, B:F.328 Hydrogen bonds: B:R.334 BOG.29: 12 residues within 4Å: Chain C: F.61, L.64, R.68, S.135, E.136, E.139, L.142, Q.143, Q.146, W.443, H.448 Ligands: NI.24 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.61, C:L.64, C:E.136 Hydrogen bonds: C:E.139, C:Q.143, C:Q.146

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 4 residues within 4Å: Chain A: S.332 Chain B: D.73, N.76, D.77 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.73, B:D.73, A:S.332

1 x NI: NICKEL (II) ION(Non-covalent)

NI.24: 3 residues within 4Å: Chain C: E.139, H.448 Ligands: BOG.29 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.139, C:E.139, C:H.448

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ntsogo Enguene, Y.V. et al., Xenon for tunnelling analysis of the efflux pump component OprN. PLoS ONE (2017)

Release Date

2017-09-20

Peptides

Multidrug efflux outer membrane protein OprN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Multidrug efflux outer membrane protein OprN

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