SMTL ID : 4lsi.1

Ion selectivity of OmpF porin soaked in 0.3M KBr

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-trimer

Ligands

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: Y.33, F.119, G.120, G.121, D.122 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.33 PEG.2: 4 residues within 4Å: Chain A: D.114, M.115, R.271, Y.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.303 Water bridges: A:Q.265, A:R.271 PEG.12: 11 residues within 4Å: Chain A: Q.67, G.68, N.69, N.70, S.71, A.76, N.80 Chain C: Y.64, K.81, T.82, R.101 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.68, A:N.70, A:N.80, A:N.80, C:T.82 Water bridges: C:R.101 PEG.13: 11 residues within 4Å: Chain A: Y.64, K.81, T.82, R.101 Chain B: Q.67, N.70, S.71, E.72, A.76, Q.77, N.80 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.82, A:R.101, B:Q.67, B:N.80 Water bridges: B:N.70 PEG.14: 3 residues within 4Å: Chain B: Y.23, F.119, D.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.23 Water bridges: B:Y.33 PEG.15: 9 residues within 4Å: Chain B: D.108, R.141, N.142, S.143, N.153, F.154, A.155, S.178, S.180 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.141, B:S.143, B:N.153, B:S.180 PEG.29: 13 residues within 4Å: Chain C: R.101, D.127, D.128, F.129, V.134, G.135, N.162, R.164, R.168, R.169, S.170, N.171, Q.201 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.101, C:D.127, C:G.135, C:N.162, C:R.164, C:Q.201 PEG.30: 11 residues within 4Å: Chain B: Y.64, K.81, T.82, R.101 Chain C: F.66, Q.67, N.70, S.71, E.72, A.76, N.80 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:T.82, C:N.70, C:N.70, C:N.80, C:N.80 Water bridges: B:R.101 PEG.31: 2 residues within 4Å: Chain C: Y.33, D.122 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.122

4 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.3: 6 residues within 4Å: Chain A: F.186, L.219, L.228, A.229, L.260, V.261 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.228, A:L.260 C8E.16: 2 residues within 4Å: Chain B: F.268, Y.302 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.268, B:F.268, B:F.268 Water bridges: B:Y.302 C8E.17: 7 residues within 4Å: Chain B: L.219, L.228, A.229, L.260, V.261, A.262, I.274 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.262, B:I.274 C8E.24: 8 residues within 4Å: Chain A: H.22, V.335 Chain C: Y.99, Y.158, L.159, G.160, D.173, G.174 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:H.22, A:V.335, C:Y.99, C:Y.99, C:Y.99 Hydrogen bonds: C:G.174

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.83, Y.103, D.114, R.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.83, A:R.83, A:D.114, A:R.133 Water bridges: A:R.43 GOL.5: 3 residues within 4Å: Chain A: N.10, K.11, V.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.12, A:V.12 GOL.18: 3 residues within 4Å: Chain B: R.83, D.114, R.133 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.83, B:R.83, B:D.114, B:R.133, B:R.133 GOL.32: 4 residues within 4Å: Chain C: R.43, R.83, D.114, R.133 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.43, C:R.43, C:R.83, C:R.83, C:R.133

8 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: E.202, Q.204, G.207 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.202, A:Q.204, A:G.207 MG.7: 3 residues within 4Å: Chain A: N.317, I.319, S.329 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.317, A:I.319, A:S.329, H2O.3, H2O.4 MG.19: 3 residues within 4Å: Chain B: E.202, Q.204, G.207 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.202, B:Q.204, B:G.207, H2O.11, H2O.14 MG.20: 4 residues within 4Å: Chain B: N.317, Q.318, I.319, S.329 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.317, B:I.319, B:S.329, H2O.11 MG.25: 3 residues within 4Å: Chain C: N.208, N.237, N.253 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:N.208, H2O.18, H2O.18 MG.26: 2 residues within 4Å: Chain C: N.70, D.75 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.75, H2O.9, H2O.20 MG.27: 3 residues within 4Å: Chain C: E.202, Q.204, G.207 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.202, C:Q.204, C:G.207, H2O.19, H2O.22 MG.28: 4 residues within 4Å: Chain C: N.317, Q.318, I.319, S.329 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:N.317, C:I.319, C:S.329

9 x BR: BROMIDE ION(Non-covalent)

BR.8: 3 residues within 4Å: Chain A: Y.125, S.126, R.168 Ligand excluded by PLIP BR.9: 2 residues within 4Å: Chain A: Y.15, K.17 Ligand excluded by PLIP BR.10: 7 residues within 4Å: Chain A: Y.103, G.104, V.105, Y.107, F.130, V.131, G.132 Ligand excluded by PLIP BR.11: 5 residues within 4Å: Chain A: M.115, L.116, P.117, Q.263, S.273 Ligand excluded by PLIP BR.21: 2 residues within 4Å: Chain B: Y.15, K.17 Ligand excluded by PLIP BR.22: 3 residues within 4Å: Chain B: Y.125, S.126, R.168 Ligand excluded by PLIP BR.23: 1 residues within 4Å: Chain B: I.52 Ligand excluded by PLIP BR.33: 2 residues within 4Å: Chain C: Y.15, K.17 Ligand excluded by PLIP BR.34: 3 residues within 4Å: Chain C: Y.125, S.126, R.168 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dhakshnamoorthy, B. et al., A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. J.Am.Chem.Soc. (2013)

Release Date

2013-10-23

Peptides

Outer membrane protein F: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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

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