SMTL ID : 3nsg.1

Crystal Structure of OmpF, an Outer Membrane Protein from Salmonella typhi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-trimer

Ligands

80 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: S.29 Ligands: SO4.2, LDA.46, GOL.131 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: W.23, N.31 Ligands: SO4.1, LDA.42, LDA.46 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Ligands: GOL.29, SO4.121 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: R.65, N.72 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: E.44, F.54, K.84 Ligand excluded by PLIP SO4.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: Y.85, E.87, V.88, G.89, N.139, S.140, D.141 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain A: A.86, E.87, V.88, F.143 Ligands: SO4.10, SO4.11 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: E.87, F.143, L.145 Ligands: SO4.9 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: F.143 Ligands: SO4.9 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: L.83, Y.85, G.89, I.91 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: A.110, P.111, T.299, Y.301 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: A.121, Y.122, Y.326 Ligand excluded by PLIP SO4.15: 1 residues within 4Å: Chain A: Y.155 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain A: Y.155 Ligands: LDA.44 Ligand excluded by PLIP SO4.17: 6 residues within 4Å: Chain A: N.159, D.161, H.163 Chain B: A.32, D.33, D.64 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Ligands: GOL.34 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: D.147, E.180, F.181, D.182 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain A: D.207, R.208 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: Q.260, Y.261, P.269, I.271 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain A: R.233, K.251, Q.280 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Ligands: GOL.39, GOL.40 Ligand excluded by PLIP SO4.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain A: Q.262, F.263, D.264, F.265, G.266, Y.301 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain A: M.1, E.2, K.304 Ligands: SO4.120 Ligand excluded by PLIP SO4.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Ligands: SO4.53, SO4.66 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain B: D.171, K.194 Ligands: SO4.52 Ligand excluded by PLIP SO4.54: 2 residues within 4Å: Chain B: N.303, K.304 Ligand excluded by PLIP SO4.55: 2 residues within 4Å: Chain B: R.60, R.77 Ligand excluded by PLIP SO4.56: 4 residues within 4Å: Chain B: A.121, Y.122, T.123 Chain C: E.67 Ligand excluded by PLIP SO4.57: 3 residues within 4Å: Chain A: N.162 Chain B: R.65, N.72 Ligand excluded by PLIP SO4.58: 7 residues within 4Å: Chain B: Y.126, I.165, Q.168, R.195, T.196, D.198, M.248 Ligand excluded by PLIP SO4.59: 7 residues within 4Å: Chain B: K.158, N.159, Q.160, H.163 Chain C: N.31, A.32, D.33 Ligand excluded by PLIP SO4.60: 2 residues within 4Å: Chain B: Q.160, N.197 Ligand excluded by PLIP SO4.61: 4 residues within 4Å: Chain B: D.147, G.148, E.180, F.181 Ligand excluded by PLIP SO4.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain B: A.220, N.221 Ligands: SO4.69 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain B: F.181, D.182 Ligands: LDA.88 Ligand excluded by PLIP SO4.65: 1 residues within 4Å: Ligands: LDA.88 Ligand excluded by PLIP SO4.66: 1 residues within 4Å: Ligands: SO4.52 Ligand excluded by PLIP SO4.67: 1 residues within 4Å: Ligands: SO4.68 Ligand excluded by PLIP SO4.68: 1 residues within 4Å: Ligands: SO4.67 Ligand excluded by PLIP SO4.69: 5 residues within 4Å: Chain B: N.221, N.222 Ligands: SO4.63, GOL.79, GOL.82 Ligand excluded by PLIP SO4.70: 3 residues within 4Å: Chain B: R.233, K.251, Q.280 Ligand excluded by PLIP SO4.71: 1 residues within 4Å: Chain B: Q.262 Ligand excluded by PLIP SO4.72: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.73: 1 residues within 4Å: Chain B: S.325 Ligand excluded by PLIP SO4.94: 2 residues within 4Å: Chain C: R.60, R.77 Ligand excluded by PLIP SO4.95: 4 residues within 4Å: Chain C: K.16, Q.38, R.60, R.77 Ligand excluded by PLIP SO4.96: 4 residues within 4Å: Chain C: Y.301, Q.340 Ligands: SO4.100, SO4.115 Ligand excluded by PLIP SO4.97: 5 residues within 4Å: Chain C: S.105, Y.106, M.109, K.217, Y.224 Ligand excluded by PLIP SO4.98: 2 residues within 4Å: Chain C: N.221, N.222 Ligand excluded by PLIP SO4.99: 1 residues within 4Å: Chain C: Q.262 Ligand excluded by PLIP SO4.100: 5 residues within 4Å: Chain C: A.110, P.111, W.309 Ligands: SO4.96, SO4.115 Ligand excluded by PLIP SO4.101: 2 residues within 4Å: Chain C: T.26, G.27 Ligand excluded by PLIP SO4.102: 3 residues within 4Å: Chain C: D.28, T.329, D.330 Ligand excluded by PLIP SO4.103: 2 residues within 4Å: Chain C: E.2, K.304 Ligand excluded by PLIP SO4.104: 1 residues within 4Å: Ligands: SO4.107 Ligand excluded by PLIP SO4.105: 1 residues within 4Å: Ligands: SO4.106 Ligand excluded by PLIP SO4.106: 5 residues within 4Å: Chain C: Y.4, N.5, K.6, D.7 Ligands: SO4.105 Ligand excluded by PLIP SO4.107: 1 residues within 4Å: Ligands: SO4.104 Ligand excluded by PLIP SO4.108: 2 residues within 4Å: Chain C: K.304, F.341 Ligand excluded by PLIP SO4.109: 3 residues within 4Å: Chain C: K.84, S.90, S.140 Ligand excluded by PLIP SO4.110: 1 residues within 4Å: Chain C: R.212 Ligand excluded by PLIP SO4.111: 2 residues within 4Å: Chain C: S.164, I.165 Ligand excluded by PLIP SO4.112: 4 residues within 4Å: Chain C: N.205, N.250, K.251, Q.280 Ligand excluded by PLIP SO4.113: 6 residues within 4Å: Chain C: N.222, Y.261, Q.262, F.263, D.264 Ligands: GOL.132 Ligand excluded by PLIP SO4.114: 6 residues within 4Å: Chain C: A.216, K.217, Y.218, L.225, A.226, A.227 Ligand excluded by PLIP SO4.115: 5 residues within 4Å: Chain C: M.109, R.268, Y.301 Ligands: SO4.96, SO4.100 Ligand excluded by PLIP SO4.116: 4 residues within 4Å: Chain C: D.289, L.317, D.318, N.320 Ligand excluded by PLIP SO4.117: 5 residues within 4Å: Chain C: L.281, N.282, G.283, G.286 Ligands: SO4.118 Ligand excluded by PLIP SO4.118: 2 residues within 4Å: Chain C: G.283 Ligands: SO4.117 Ligand excluded by PLIP SO4.119: 6 residues within 4Å: Chain B: Y.4, N.9, K.10, E.44 Chain C: N.305, F.341 Ligand excluded by PLIP SO4.120: 5 residues within 4Å: Chain A: M.1, K.304, N.305 Chain C: Y.4 Ligands: SO4.26 Ligand excluded by PLIP SO4.121: 3 residues within 4Å: Chain C: D.161, N.162 Ligands: SO4.3 Ligand excluded by PLIP SO4.122: 2 residues within 4Å: Chain C: N.48, T.49 Ligand excluded by PLIP SO4.123: 2 residues within 4Å: Ligands: FLC.144, TAM.146 Ligand excluded by PLIP SO4.124: 1 residues within 4Å: Ligands: GOL.147 Ligand excluded by PLIP

38 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 7 residues within 4Å: Chain A: K.16, Y.36, Q.38, E.58, R.60, R.77 Ligands: TAM.48 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain A: S.324, V.327 Ligands: SO4.3 Ligand excluded by PLIP GOL.30: 1 residues within 4Å: Chain A: K.194 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain A: Q.160, N.197 Ligand excluded by PLIP GOL.32: 2 residues within 4Å: Chain A: D.161, N.162 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain A: D.171, N.192, S.193, K.194, R.208 Ligands: TAM.49 Ligand excluded by PLIP GOL.34: 2 residues within 4Å: Ligands: SO4.18, TLA.51 Ligand excluded by PLIP GOL.35: 1 residues within 4Å: Ligands: TLA.51 Ligand excluded by PLIP GOL.36: 2 residues within 4Å: Ligands: TAM.49, TLA.51 Ligand excluded by PLIP GOL.37: 2 residues within 4Å: Chain A: Y.175, Y.190 Ligand excluded by PLIP GOL.38: 2 residues within 4Å: Chain A: V.223, Y.261 Ligand excluded by PLIP GOL.39: 1 residues within 4Å: Ligands: SO4.23 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain A: Y.261, F.263, D.264 Ligands: SO4.23 Ligand excluded by PLIP GOL.41: 2 residues within 4Å: Chain A: K.279 Ligands: LDA.47 Ligand excluded by PLIP GOL.74: 4 residues within 4Å: Chain B: M.1, E.2, N.5 Ligands: TLA.93 Ligand excluded by PLIP GOL.75: 10 residues within 4Å: Chain B: Y.85, A.86, E.87, G.89, S.90, R.138, N.139, S.140, D.141, G.144 Ligand excluded by PLIP GOL.76: 1 residues within 4Å: Chain B: E.87 Ligand excluded by PLIP GOL.77: 4 residues within 4Å: Chain B: G.144, L.145, V.146, D.147 Ligand excluded by PLIP GOL.78: 2 residues within 4Å: Chain B: D.182, N.221 Ligand excluded by PLIP GOL.79: 1 residues within 4Å: Ligands: SO4.69 Ligand excluded by PLIP GOL.80: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.81: 1 residues within 4Å: Chain B: R.208 Ligand excluded by PLIP GOL.82: 3 residues within 4Å: Chain B: N.221, N.222 Ligands: SO4.69 Ligand excluded by PLIP GOL.83: 6 residues within 4Å: Chain B: K.277, K.279, S.287, A.288, D.289 Ligands: GOL.84 Ligand excluded by PLIP GOL.84: 2 residues within 4Å: Chain B: S.287 Ligands: GOL.83 Ligand excluded by PLIP GOL.125: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.126: 1 residues within 4Å: Chain C: E.180 Ligand excluded by PLIP GOL.127: 5 residues within 4Å: Chain C: Q.200, D.201, R.202, T.245 Ligands: TAM.138 Ligand excluded by PLIP GOL.128: 2 residues within 4Å: Chain C: T.243 Ligands: TAM.138 Ligand excluded by PLIP GOL.129: 2 residues within 4Å: Ligands: TAM.138, FLC.140 Ligand excluded by PLIP GOL.130: 3 residues within 4Å: Chain C: N.192, R.208 Ligands: GOL.142 Ligand excluded by PLIP GOL.131: 4 residues within 4Å: Chain C: D.171 Ligands: SO4.1, TAM.139, GOL.142 Ligand excluded by PLIP GOL.132: 3 residues within 4Å: Chain C: F.263, D.264 Ligands: SO4.113 Ligand excluded by PLIP GOL.133: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.142: 7 residues within 4Å: Chain C: D.171, N.192, K.194, R.208 Ligands: GOL.130, GOL.131, TAM.139 Ligand excluded by PLIP GOL.143: 1 residues within 4Å: Ligands: TAM.146 Ligand excluded by PLIP GOL.145: 1 residues within 4Å: Ligands: TAM.139 Ligand excluded by PLIP GOL.147: 3 residues within 4Å: Ligands: SO4.124, FLC.144, TAM.146 Ligand excluded by PLIP

17 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)(Non-functional Binders)

LDA.42: 12 residues within 4Å: Chain A: H.21, W.23, N.31, V.335, I.337 Chain C: L.83, I.91, Y.93, L.135, G.157, D.171 Ligands: SO4.2 Ligand excluded by PLIP LDA.43: 2 residues within 4Å: Chain A: L.145 Ligands: LDA.45 Ligand excluded by PLIP LDA.44: 11 residues within 4Å: Chain A: L.83, I.91, Y.93, L.135, G.157 Chain B: H.21, W.23, N.31, V.335, I.337 Ligands: SO4.16 Ligand excluded by PLIP LDA.45: 3 residues within 4Å: Chain A: Y.179, D.182 Ligands: LDA.43 Ligand excluded by PLIP LDA.46: 7 residues within 4Å: Chain A: W.23, T.24, T.25, S.29, V.335 Ligands: SO4.1, SO4.2 Ligand excluded by PLIP LDA.47: 3 residues within 4Å: Chain A: Y.229, L.255 Ligands: GOL.41 Ligand excluded by PLIP LDA.85: 5 residues within 4Å: Chain B: V.88, L.135, Y.155 Ligands: LDA.134, LDA.136 Ligand excluded by PLIP LDA.86: 2 residues within 4Å: Chain B: L.145 Ligands: LDA.87 Ligand excluded by PLIP LDA.87: 4 residues within 4Å: Chain B: V.146 Ligands: LDA.86, LDA.88, LDA.89 Ligand excluded by PLIP LDA.88: 5 residues within 4Å: Chain B: L.149, Y.179 Ligands: SO4.64, SO4.65, LDA.87 Ligand excluded by PLIP LDA.89: 1 residues within 4Å: Ligands: LDA.87 Ligand excluded by PLIP LDA.90: 4 residues within 4Å: Chain B: Y.273, Q.275, K.277, K.292 Ligand excluded by PLIP LDA.91: 3 residues within 4Å: Chain B: I.294, F.314, L.316 Ligand excluded by PLIP LDA.134: 6 residues within 4Å: Chain B: I.91 Chain C: W.23, N.31 Ligands: LDA.85, LDA.135, LDA.136 Ligand excluded by PLIP LDA.135: 6 residues within 4Å: Chain C: W.23, T.24, T.25, S.29, V.310 Ligands: LDA.134 Ligand excluded by PLIP LDA.136: 13 residues within 4Å: Chain B: I.91, Y.93, G.133, L.135, Y.155, Q.156, G.157 Chain C: H.21, W.23, V.335, I.337 Ligands: LDA.85, LDA.134 Ligand excluded by PLIP LDA.137: 9 residues within 4Å: Chain A: K.30, N.31, A.32, D.33, D.64 Chain C: K.158, N.159, Q.160, D.161 Ligand excluded by PLIP

6 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)(Non-functional Binders)

TAM.48: 6 residues within 4Å: Chain A: R.20, R.60, R.77, S.114, R.130 Ligands: GOL.28 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.20, A:R.60, A:R.77, A:R.77, A:R.130, A:R.130 TAM.49: 5 residues within 4Å: Chain A: K.194, D.207, R.208 Ligands: GOL.33, GOL.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.207, A:R.208, A:R.208 Water bridges: A:K.194 TAM.92: 2 residues within 4Å: Chain B: G.206, D.207 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.206 TAM.138: 7 residues within 4Å: Chain C: T.243, D.244, T.245 Ligands: GOL.127, GOL.128, GOL.129, FLC.140 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.202, C:T.243, C:D.244 TAM.139: 3 residues within 4Å: Ligands: GOL.131, GOL.142, GOL.145 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.171, C:D.171 TAM.146: 4 residues within 4Å: Ligands: SO4.123, GOL.143, FLC.144, GOL.147 No protein-ligand interaction detected (PLIP)

4 x FLC: CITRATE ANION(Non-functional Binders)(Non-covalent)

FLC.50: 1 residues within 4Å: Ligands: TLA.51 No protein-ligand interaction detected (PLIP) FLC.140: 3 residues within 4Å: Chain C: D.244 Ligands: GOL.129, TAM.138 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.244 Hydrogen bonds: C:D.244, C:D.244 Water bridges: C:D.244 FLC.141: 3 residues within 4Å: Chain C: Q.275, D.289, K.292 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.275, C:D.289 Water bridges: C:K.277 Salt bridges: C:K.277, C:K.277, C:K.292 FLC.144: 3 residues within 4Å: Ligands: SO4.123, TAM.146, GOL.147 No protein-ligand interaction detected (PLIP)

2 x TLA: L(+)-TARTARIC ACID(Non-functional Binders)(Non-covalent)

TLA.51: 4 residues within 4Å: Ligands: GOL.34, GOL.35, GOL.36, FLC.50 No protein-ligand interaction detected (PLIP) TLA.93: 2 residues within 4Å: Chain A: Y.4 Ligands: GOL.74 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.304 Water bridges: A:Y.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balasubramaniam, D. et al., Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi. J.Struct.Biol. (2012)

Release Date

2011-07-13

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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