SMTL ID : 3poq.1

Crystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, small unit cell

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

69 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)(Non-functional Binders)

OLC.1: 9 residues within 4Å: Chain A: Y.98, Y.157, G.159, K.160, D.172 Chain C: H.21, V.334, I.336 Ligands: OLC.70 Ligand excluded by PLIP OLC.2: 10 residues within 4Å: Chain A: G.176, S.177, G.189, A.190, Y.191, E.212, W.214, T.216 Ligands: OLC.19, OLC.20 Ligand excluded by PLIP OLC.3: 2 residues within 4Å: Chain A: F.185 Ligands: OLC.23 Ligand excluded by PLIP OLC.4: 5 residues within 4Å: Chain A: L.218, K.219, L.227, L.259 Ligands: OLC.5 Ligand excluded by PLIP OLC.5: 8 residues within 4Å: Chain A: L.259, A.261, I.273, A.274, Y.275, F.295 Ligands: OLC.4, OLC.8 Ligand excluded by PLIP OLC.6: 6 residues within 4Å: Chain A: I.225, L.227, A.261, Q.262, I.273 Ligands: OLC.7 Ligand excluded by PLIP OLC.7: 6 residues within 4Å: Chain A: Y.263, F.265, L.269, P.271 Ligands: OLC.6, OLC.10 Ligand excluded by PLIP OLC.8: 4 residues within 4Å: Chain A: I.315, Q.317 Ligands: OLC.5, OLC.9 Ligand excluded by PLIP OLC.9: 2 residues within 4Å: Chain A: I.315 Ligands: OLC.8 Ligand excluded by PLIP OLC.10: 1 residues within 4Å: Ligands: OLC.7 Ligand excluded by PLIP OLC.11: 3 residues within 4Å: Chain A: L.259, Y.275, K.277 Ligand excluded by PLIP OLC.12: 5 residues within 4Å: Chain A: Y.180 Ligands: OLC.13, OLC.16, OLC.20, OLC.21 Ligand excluded by PLIP OLC.13: 3 residues within 4Å: Chain A: L.151 Ligands: OLC.12, OLC.14 Ligand excluded by PLIP OLC.14: 4 residues within 4Å: Chain A: F.144, L.147, V.148 Ligands: OLC.13 Ligand excluded by PLIP OLC.15: 5 residues within 4Å: Chain A: Y.182, F.185, I.187 Ligands: OLC.17, OLC.21 Ligand excluded by PLIP OLC.16: 3 residues within 4Å: Ligands: OLC.12, OLC.17, OLC.21 Ligand excluded by PLIP OLC.17: 2 residues within 4Å: Ligands: OLC.15, OLC.16 Ligand excluded by PLIP OLC.18: 2 residues within 4Å: Chain B: F.96 Ligands: OLC.27 Ligand excluded by PLIP OLC.19: 2 residues within 4Å: Chain A: I.178 Ligands: OLC.2 Ligand excluded by PLIP OLC.20: 11 residues within 4Å: Chain A: I.178, S.179, Y.180, I.187, G.189, W.214, T.216 Ligands: OLC.2, OLC.12, OLC.21, OLC.23 Ligand excluded by PLIP OLC.21: 5 residues within 4Å: Chain A: I.187 Ligands: OLC.12, OLC.15, OLC.16, OLC.20 Ligand excluded by PLIP OLC.22: 5 residues within 4Å: Chain A: F.23, S.24, K.25, Y.313, V.332 Ligand excluded by PLIP OLC.23: 4 residues within 4Å: Chain A: T.216, Y.231 Ligands: OLC.3, OLC.20 Ligand excluded by PLIP OLC.27: 9 residues within 4Å: Chain A: H.21, V.334, I.336 Chain B: Y.98, Y.157, G.159, K.160, D.172 Ligands: OLC.18 Ligand excluded by PLIP OLC.28: 10 residues within 4Å: Chain B: G.176, S.177, G.189, A.190, Y.191, E.212, W.214, T.216 Ligands: OLC.45, OLC.46 Ligand excluded by PLIP OLC.29: 2 residues within 4Å: Chain B: F.185 Ligands: OLC.49 Ligand excluded by PLIP OLC.30: 5 residues within 4Å: Chain B: L.218, K.219, L.227, L.259 Ligands: OLC.31 Ligand excluded by PLIP OLC.31: 8 residues within 4Å: Chain B: L.259, A.261, I.273, A.274, Y.275, F.295 Ligands: OLC.30, OLC.34 Ligand excluded by PLIP OLC.32: 6 residues within 4Å: Chain B: I.225, L.227, A.261, Q.262, I.273 Ligands: OLC.33 Ligand excluded by PLIP OLC.33: 6 residues within 4Å: Chain B: Y.263, F.265, L.269, P.271 Ligands: OLC.32, OLC.36 Ligand excluded by PLIP OLC.34: 4 residues within 4Å: Chain B: I.315, Q.317 Ligands: OLC.31, OLC.35 Ligand excluded by PLIP OLC.35: 2 residues within 4Å: Chain B: I.315 Ligands: OLC.34 Ligand excluded by PLIP OLC.36: 1 residues within 4Å: Ligands: OLC.33 Ligand excluded by PLIP OLC.37: 3 residues within 4Å: Chain B: L.259, Y.275, K.277 Ligand excluded by PLIP OLC.38: 5 residues within 4Å: Chain B: Y.180 Ligands: OLC.39, OLC.42, OLC.46, OLC.47 Ligand excluded by PLIP OLC.39: 3 residues within 4Å: Chain B: L.151 Ligands: OLC.38, OLC.40 Ligand excluded by PLIP OLC.40: 4 residues within 4Å: Chain B: F.144, L.147, V.148 Ligands: OLC.39 Ligand excluded by PLIP OLC.41: 5 residues within 4Å: Chain B: Y.182, F.185, I.187 Ligands: OLC.43, OLC.47 Ligand excluded by PLIP OLC.42: 3 residues within 4Å: Ligands: OLC.38, OLC.43, OLC.47 Ligand excluded by PLIP OLC.43: 2 residues within 4Å: Ligands: OLC.41, OLC.42 Ligand excluded by PLIP OLC.44: 2 residues within 4Å: Chain C: F.96 Ligands: OLC.53 Ligand excluded by PLIP OLC.45: 2 residues within 4Å: Chain B: I.178 Ligands: OLC.28 Ligand excluded by PLIP OLC.46: 11 residues within 4Å: Chain B: I.178, S.179, Y.180, I.187, G.189, W.214, T.216 Ligands: OLC.28, OLC.38, OLC.47, OLC.49 Ligand excluded by PLIP OLC.47: 5 residues within 4Å: Chain B: I.187 Ligands: OLC.38, OLC.41, OLC.42, OLC.46 Ligand excluded by PLIP OLC.48: 5 residues within 4Å: Chain B: F.23, S.24, K.25, Y.313, V.332 Ligand excluded by PLIP OLC.49: 4 residues within 4Å: Chain B: T.216, Y.231 Ligands: OLC.29, OLC.46 Ligand excluded by PLIP OLC.53: 9 residues within 4Å: Chain B: H.21, V.334, I.336 Chain C: Y.98, Y.157, G.159, K.160, D.172 Ligands: OLC.44 Ligand excluded by PLIP OLC.54: 10 residues within 4Å: Chain C: G.176, S.177, G.189, A.190, Y.191, E.212, W.214, T.216 Ligands: OLC.71, OLC.72 Ligand excluded by PLIP OLC.55: 2 residues within 4Å: Chain C: F.185 Ligands: OLC.75 Ligand excluded by PLIP OLC.56: 5 residues within 4Å: Chain C: L.218, K.219, L.227, L.259 Ligands: OLC.57 Ligand excluded by PLIP OLC.57: 8 residues within 4Å: Chain C: L.259, A.261, I.273, A.274, Y.275, F.295 Ligands: OLC.56, OLC.60 Ligand excluded by PLIP OLC.58: 6 residues within 4Å: Chain C: I.225, L.227, A.261, Q.262, I.273 Ligands: OLC.59 Ligand excluded by PLIP OLC.59: 6 residues within 4Å: Chain C: Y.263, F.265, L.269, P.271 Ligands: OLC.58, OLC.62 Ligand excluded by PLIP OLC.60: 4 residues within 4Å: Chain C: I.315, Q.317 Ligands: OLC.57, OLC.61 Ligand excluded by PLIP OLC.61: 2 residues within 4Å: Chain C: I.315 Ligands: OLC.60 Ligand excluded by PLIP OLC.62: 1 residues within 4Å: Ligands: OLC.59 Ligand excluded by PLIP OLC.63: 3 residues within 4Å: Chain C: L.259, Y.275, K.277 Ligand excluded by PLIP OLC.64: 5 residues within 4Å: Chain C: Y.180 Ligands: OLC.65, OLC.68, OLC.72, OLC.73 Ligand excluded by PLIP OLC.65: 3 residues within 4Å: Chain C: L.151 Ligands: OLC.64, OLC.66 Ligand excluded by PLIP OLC.66: 4 residues within 4Å: Chain C: F.144, L.147, V.148 Ligands: OLC.65 Ligand excluded by PLIP OLC.67: 5 residues within 4Å: Chain C: Y.182, F.185, I.187 Ligands: OLC.69, OLC.73 Ligand excluded by PLIP OLC.68: 3 residues within 4Å: Ligands: OLC.64, OLC.69, OLC.73 Ligand excluded by PLIP OLC.69: 2 residues within 4Å: Ligands: OLC.67, OLC.68 Ligand excluded by PLIP OLC.70: 2 residues within 4Å: Chain A: F.96 Ligands: OLC.1 Ligand excluded by PLIP OLC.71: 2 residues within 4Å: Chain C: I.178 Ligands: OLC.54 Ligand excluded by PLIP OLC.72: 11 residues within 4Å: Chain C: I.178, S.179, Y.180, I.187, G.189, W.214, T.216 Ligands: OLC.54, OLC.64, OLC.73, OLC.75 Ligand excluded by PLIP OLC.73: 5 residues within 4Å: Chain C: I.187 Ligands: OLC.64, OLC.67, OLC.68, OLC.72 Ligand excluded by PLIP OLC.74: 5 residues within 4Å: Chain C: F.23, S.24, K.25, Y.313, V.332 Ligand excluded by PLIP OLC.75: 4 residues within 4Å: Chain C: T.216, Y.231 Ligands: OLC.55, OLC.72 Ligand excluded by PLIP

9 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.24: 7 residues within 4Å: Chain A: Y.102, Y.106, A.123, Y.124, S.125, G.131, R.132 No protein-ligand interaction detected (PLIP) SCN.25: 6 residues within 4Å: Chain A: S.70, D.74 Chain B: R.163, D.164, T.165, R.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.70 SCN.26: 5 residues within 4Å: Chain A: R.167, Q.203, P.239, S.248, G.249 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.166 SCN.50: 7 residues within 4Å: Chain B: Y.102, Y.106, A.123, Y.124, S.125, G.131, R.132 No protein-ligand interaction detected (PLIP) SCN.51: 6 residues within 4Å: Chain B: S.70, D.74 Chain C: R.163, D.164, T.165, R.168 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.70 SCN.52: 5 residues within 4Å: Chain B: R.167, Q.203, P.239, S.248, G.249 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.166 SCN.76: 7 residues within 4Å: Chain C: Y.102, Y.106, A.123, Y.124, S.125, G.131, R.132 No protein-ligand interaction detected (PLIP) SCN.77: 6 residues within 4Å: Chain A: R.163, D.164, T.165, R.168 Chain C: S.70, D.74 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.70 SCN.78: 5 residues within 4Å: Chain C: R.167, Q.203, P.239, S.248, G.249 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Efremov, R.G. et al., Structure of Escherichia coli OmpF porin from lipidic mesophase. J.Struct.Biol. (2012)

Release Date

2012-03-07

Peptides

OmpF protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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OmpF protein

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