SMTL ID : 3pox.2 (1 other biounit)

Crystal Structure of E.coli OmpF porin in lipidic cubic phase: space group P1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

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

OLC.1: 6 residues within 4Å: Chain A: V.174, G.175, G.176, Y.191 Ligands: OLC.2, OLC.5 Ligand excluded by PLIP OLC.2: 10 residues within 4Å: Chain A: F.153, G.176, S.177, I.178, G.189, A.190, W.214, R.235 Ligands: OLC.1, OLC.5 Ligand excluded by PLIP OLC.3: 4 residues within 4Å: Chain A: L.259, Y.275, F.295 Ligands: OLC.6 Ligand excluded by PLIP OLC.4: 4 residues within 4Å: Chain A: I.225, A.261, P.271, I.273 Ligand excluded by PLIP OLC.5: 4 residues within 4Å: Chain A: Y.191, E.212 Ligands: OLC.1, OLC.2 Ligand excluded by PLIP OLC.6: 10 residues within 4Å: Chain A: L.218, K.219, Y.220, L.227, A.228, A.229, L.259, V.260, A.274 Ligands: OLC.3 Ligand excluded by PLIP OLC.7: 4 residues within 4Å: Chain A: L.151, I.178, I.187, G.189 Ligand excluded by PLIP OLC.8: 6 residues within 4Å: Chain A: T.216, G.217, L.218, A.229, Y.231, V.257 Ligand excluded by PLIP OLC.9: 6 residues within 4Å: Chain A: F.267, Y.301 Chain B: Y.90, G.94, F.96 Ligands: K.12 Ligand excluded by PLIP OLC.15: 15 residues within 4Å: Chain A: H.21, F.23, A.299, T.300, Y.301, T.309, Y.310, V.311, V.334, I.336 Chain B: Y.98, Y.157, G.159, K.160, D.172 Ligand excluded by PLIP OLC.16: 3 residues within 4Å: Chain B: L.259, Y.275, F.295 Ligand excluded by PLIP OLC.17: 3 residues within 4Å: Chain B: Y.313, D.330 Ligands: OLC.18 Ligand excluded by PLIP OLC.18: 5 residues within 4Å: Chain B: K.25, Y.313, D.329, D.330 Ligands: OLC.17 Ligand excluded by PLIP OLC.19: 4 residues within 4Å: Chain B: F.23, Y.313, D.330, V.332 Ligand excluded by PLIP OLC.20: 3 residues within 4Å: Chain B: F.23 Ligands: OLC.21, OLC.34 Ligand excluded by PLIP OLC.21: 17 residues within 4Å: Chain B: H.21, F.23, L.269, A.299, Y.301, T.309, Y.310, V.311, V.334, I.336 Chain C: Y.98, Y.157, G.159, K.160, D.172 Ligands: OLC.20, OLC.22 Ligand excluded by PLIP OLC.22: 5 residues within 4Å: Chain B: Y.301, T.309 Chain C: L.88, F.96 Ligands: OLC.21 Ligand excluded by PLIP OLC.28: 4 residues within 4Å: Chain C: V.174, Y.191, A.193 Ligands: OLC.29 Ligand excluded by PLIP OLC.29: 8 residues within 4Å: Chain C: G.176, S.177, I.178, G.189, A.190, Y.191, W.214 Ligands: OLC.28 Ligand excluded by PLIP OLC.30: 8 residues within 4Å: Chain C: L.151, I.178, S.179, Y.180, I.187, V.188, G.189, T.216 Ligand excluded by PLIP OLC.31: 3 residues within 4Å: Chain C: L.218, L.259 Ligands: OLC.32 Ligand excluded by PLIP OLC.32: 8 residues within 4Å: Chain C: K.219, Y.220, L.227, A.228, L.259, V.260, A.261 Ligands: OLC.31 Ligand excluded by PLIP OLC.33: 4 residues within 4Å: Chain C: A.261, Q.262, Y.263, P.271 Ligand excluded by PLIP OLC.34: 3 residues within 4Å: Chain C: F.96, Y.157 Ligands: OLC.20 Ligand excluded by PLIP OLC.35: 6 residues within 4Å: Chain C: N.52, L.88, Y.90, G.94, S.95, F.96 Ligand excluded by PLIP

10 x K: POTASSIUM ION(Non-covalent)

K.10: 3 residues within 4Å: Chain A: N.316, I.318, S.328 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.316, A:I.318, A:S.328 K.11: 3 residues within 4Å: Chain A: E.201, Q.203, G.206 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.201, A:Q.203, H2O.7, H2O.9, H2O.10 K.12: 5 residues within 4Å: Chain A: F.267, Y.301, Y.302, F.303 Ligands: OLC.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:F.267, A:Y.302 K.13: 3 residues within 4Å: Chain A: N.207, N.236, N.252 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.207, H2O.5, H2O.7 K.23: 3 residues within 4Å: Chain B: N.316, I.318, S.328 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.316, B:I.318, B:S.328, H2O.12, H2O.22 K.24: 3 residues within 4Å: Chain B: E.201, Q.203, G.206 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.201, B:Q.203, B:G.206, H2O.15, H2O.19 K.25: 3 residues within 4Å: Chain B: N.207, N.236, N.252 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:N.207, H2O.14, H2O.14, H2O.18 K.36: 3 residues within 4Å: Chain C: N.316, I.318, S.328 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:N.316, C:I.318, C:S.328, H2O.23, H2O.30 K.37: 3 residues within 4Å: Chain C: E.201, Q.203, G.206 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.201, C:Q.203, C:G.206, H2O.27, H2O.30 K.38: 3 residues within 4Å: Chain C: N.207, N.236, N.252 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:N.207, H2O.24, H2O.27, H2O.30

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

SCN.14: 5 residues within 4Å: Chain A: Y.14, G.15, K.16, R.42, E.62 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.15 SCN.26: 5 residues within 4Å: Chain B: Y.14, G.15, K.16, R.42, E.62 No protein-ligand interaction detected (PLIP) SCN.27: 5 residues within 4Å: Chain B: S.70, D.74 Chain C: D.164, T.165, R.168 No protein-ligand interaction detected (PLIP) SCN.39: 5 residues within 4Å: Chain C: Y.14, G.15, K.16, R.42, E.62 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.15

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
D

B
E

C
F

Membrane

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

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