SMTL ID : 6zhp.1

Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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.3, H2O.5 MG.5: 3 residues within 4Å: Chain B: N.229, N.258, N.274 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:N.229, H2O.8, H2O.9, H2O.11 MG.9: 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.14, H2O.14, H2O.17

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

QLB.2: 10 residues within 4Å: Chain A: I.200, S.201, Y.202, I.209, V.210, G.211, T.238, G.239, L.240, Y.253 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.200 Hydrogen bonds: A:T.238 Water bridges: A:T.238 QLB.3: 9 residues within 4Å: Chain A: L.281, V.282, A.283, I.295, A.296, Y.297, F.317, I.337, Q.339 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.281, A:A.283, A:F.317 Hydrogen bonds: A:Q.339 QLB.6: 10 residues within 4Å: Chain B: I.200, S.201, Y.202, I.209, V.210, G.211, T.238, G.239, L.240, Y.253 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.200 Hydrogen bonds: B:T.238 Water bridges: B:T.238 QLB.7: 9 residues within 4Å: Chain B: L.281, V.282, A.283, I.295, A.296, Y.297, F.317, I.337, Q.339 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.281, B:A.283, B:F.317 Hydrogen bonds: B:Q.339 QLB.10: 10 residues within 4Å: Chain C: I.200, S.201, Y.202, I.209, V.210, G.211, T.238, G.239, L.240, Y.253 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.200 Hydrogen bonds: C:T.238 Water bridges: C:T.238 QLB.11: 9 residues within 4Å: Chain C: L.281, V.282, A.283, I.295, A.296, Y.297, F.317, I.337, Q.339 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.281, C:A.283, C:F.317 Hydrogen bonds: C:Q.339

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

NA.4: 4 residues within 4Å: Chain A: E.223, Q.225, P.226, G.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.226 NA.8: 4 residues within 4Å: Chain B: E.223, Q.225, P.226, G.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.223 NA.12: 4 residues within 4Å: Chain C: E.223, Q.225, P.226, G.228 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.223

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
B

C
B

Membrane

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

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