SMTL ID : 6zhv.1

Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: N.229, N.258, N.274 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.229, H2O.2, H2O.2, H2O.2 MG.8: 3 residues within 4Å: Chain B: N.229, N.258, N.274 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.229, H2O.4 MG.15: 3 residues within 4Å: Chain C: N.229, N.258, N.274 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:N.229, H2O.7, H2O.7, H2O.7

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

NA.2: 3 residues within 4Å: Chain A: A.97 Chain B: K.102, T.103 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.97, B:T.103, B:T.103 NA.3: 4 residues within 4Å: Chain A: Y.85, F.87 Chain B: Y.85 Chain C: F.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.85 NA.4: 3 residues within 4Å: Chain A: N.338, I.340, S.350 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.338 NA.5: 3 residues within 4Å: Chain A: E.223, Q.225, G.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.225 NA.6: 5 residues within 4Å: Chain A: R.218, Q.222, L.227, G.228, F.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.218, A:R.218, A:G.228, A:F.272 NA.9: 3 residues within 4Å: Chain B: E.223, Q.225, G.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.228 NA.10: 5 residues within 4Å: Chain B: D.312, N.315, Q.339, I.340, D.341 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.312, B:N.315, B:D.341 Water bridges: B:D.341 NA.11: 5 residues within 4Å: Chain B: N.328, M.329, S.330, V.359, Q.361 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.330 NA.12: 6 residues within 4Å: Chain B: R.218, Q.222, Q.225, L.227, G.228, F.272 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.218, B:R.218, B:L.227, B:F.272 NA.16: 3 residues within 4Å: Chain C: E.223, Q.225, G.228 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.225 NA.17: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.88 Water bridges: C:Q.88 NA.18: 6 residues within 4Å: Chain C: R.218, Q.222, Q.225, L.227, G.228, F.272 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.218, C:R.218, C:Q.222, C:F.272

7 x QLB: 2-[2-(2-octoxyethoxy)ethoxy]ethanol(Non-covalent)

QLB.7: 17 residues within 4Å: Chain A: G.41, H.43, F.45, T.331, Y.332, V.333, V.356, G.357, I.358 Chain B: F.118, Y.120, A.159, Y.179, L.180, G.181, D.194, G.195 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.333, A:V.356 QLB.13: 13 residues within 4Å: Chain B: G.41, H.43, L.291, A.321, Y.323, T.331, Y.332, V.333, V.356, G.357, I.358 Chain C: F.118, Y.120 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.291, B:V.356 QLB.14: 16 residues within 4Å: Chain B: L.240, K.241, Y.242, L.249, A.250, A.251, L.281, V.282, A.283, I.295, A.296, Y.297, F.317, E.318, V.319, I.337 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.240, B:L.249, B:A.283 QLB.19: 12 residues within 4Å: Chain C: F.166, L.173, F.175, A.176, V.177, G.198, S.199, I.200, G.211, A.212, Y.213 Ligands: QLB.20 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.166, C:I.200 QLB.20: 11 residues within 4Å: Chain C: D.194, G.195, V.196, G.197, G.198, Y.213, A.215, A.216, D.217, K.232 Ligands: QLB.19 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.196 Hydrogen bonds: C:K.232 QLB.21: 14 residues within 4Å: Chain A: F.118, Y.120, A.159, Y.179, L.180, G.181, D.194, G.195, V.196 Chain C: H.43, F.45, V.356, G.357, I.358 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.356, A:Y.120, A:Y.120, A:Y.120 QLB.22: 13 residues within 4Å: Chain C: F.207, L.240, K.241, Y.242, L.249, A.250, A.251, L.281, V.282, A.283, I.295, A.296, Y.297 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sousa, C.F. et al., Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic. To Be Published

Release Date

2021-05-05

Peptides

Outer membrane porin F: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Membrane

We predict this structure to be a membrane protein.
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Outer membrane porin F

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