SMTL ID : 7cz9.1 (1 other biounit)

Crystal structure of multidrug efflux transporter OqxB from Klebsiella pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

33 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 7 residues within 4Å: Chain A: Y.387, L.388, G.390 Chain B: V.456 Ligands: LMT.9, LMT.30, LMT.31 Ligand excluded by PLIP LMT.2: 14 residues within 4Å: Chain A: M.1, F.3, G.442, A.446, L.449, A.896, L.897, E.899, R.956, E.957, I.960 Chain C: R.10, F.13 Ligands: LMT.40 Ligand excluded by PLIP LMT.3: 13 residues within 4Å: Chain A: D.9, R.10, P.11, I.12, A.15, I.19, F.22, I.373, V.377, L.497 Chain B: E.899, W.901 Ligands: PTY.32 Ligand excluded by PLIP LMT.4: 21 residues within 4Å: Chain A: K.81, T.93, P.329, Y.330, Y.579, I.581, V.616, A.623, L.624, Q.625, F.626, F.636, G.638, P.674, I.676, L.677, G.678, L.679, G.680, D.867 Ligands: LMT.5 Ligand excluded by PLIP LMT.5: 14 residues within 4Å: Chain A: Q.46, R.48, Q.134, V.141, R.157, Q.176, Q.178, I.179, F.180, L.280, F.295, F.626 Ligands: LMT.4, GOL.19 Ligand excluded by PLIP LMT.6: 11 residues within 4Å: Chain A: I.29, N.301, I.303, D.304, N.307, R.337, I.340, V.344, L.347, L.348, F.383 Ligand excluded by PLIP LMT.7: 9 residues within 4Å: Chain A: M.458, F.564, N.877, F.883, V.887, N.929, Q.934, V.938 Ligands: LMT.8 Ligand excluded by PLIP LMT.8: 20 residues within 4Å: Chain A: F.455, M.458, L.461, Y.469, F.472, A.473, I.476, G.569, G.570, F.571, S.842, Q.872, Q.875, N.877, F.883, Q.934, V.935, V.938, V.939 Ligands: LMT.7 Ligand excluded by PLIP LMT.9: 14 residues within 4Å: Chain A: P.38, D.39, P.298, L.389, G.390, S.392, V.456, K.470, Q.471, A.477, I.478, V.481 Ligands: LMT.1, LMT.45 Ligand excluded by PLIP LMT.10: 15 residues within 4Å: Chain A: R.170, R.771 Chain B: T.65, E.68, E.69, N.72, M.78, M.80, R.97, R.822, N.824, G.825, F.870, T.874 Ligands: GOL.17 Ligand excluded by PLIP LMT.11: 21 residues within 4Å: Chain A: E.36, Y.37, F.335, D.338, S.339, A.342, T.395, F.399, V.402, L.403, G.406, Q.575, K.577, F.932, A.986, F.987, L.994, A.1000, G.1001, R.1005, T.1008 Ligand excluded by PLIP LMT.22: 5 residues within 4Å: Chain B: L.31, P.33, Y.387, L.388, G.390 Ligand excluded by PLIP LMT.23: 21 residues within 4Å: Chain B: K.81, T.93, P.329, Y.330, Y.579, I.581, V.616, A.623, L.624, Q.625, F.626, F.636, G.638, P.674, I.676, L.677, G.678, L.679, G.680, Q.681 Ligands: LMT.26 Ligand excluded by PLIP LMT.24: 18 residues within 4Å: Chain B: E.36, Y.37, F.335, D.338, S.339, A.342, T.395, F.399, V.402, Q.575, K.577, A.986, F.987, L.994, G.1001, V.1004, R.1005, T.1008 Ligand excluded by PLIP LMT.25: 12 residues within 4Å: Chain A: R.10, F.13, V.16 Chain B: M.1, F.3, G.442, A.896, L.897, E.899, R.956, E.957 Ligands: GOL.34 Ligand excluded by PLIP LMT.26: 15 residues within 4Å: Chain B: Q.46, Q.134, V.141, R.157, Q.176, Q.178, I.179, F.180, G.181, L.280, F.295, F.618, F.626, N.628 Ligands: LMT.23 Ligand excluded by PLIP LMT.27: 10 residues within 4Å: Chain B: N.301, I.303, D.304, N.307, I.340, V.344, L.347, V.380, F.383, L.393 Ligand excluded by PLIP LMT.28: 8 residues within 4Å: Chain B: V.454, M.458, F.564, F.883, M.915, N.929, Q.934 Ligands: LMT.29 Ligand excluded by PLIP LMT.29: 8 residues within 4Å: Chain B: M.458, L.461, Y.469, N.877, F.883, V.935, V.938 Ligands: LMT.28 Ligand excluded by PLIP LMT.30: 8 residues within 4Å: Chain B: D.39, L.389, G.390, F.391, K.470, Q.471, V.481 Ligands: LMT.1 Ligand excluded by PLIP LMT.31: 8 residues within 4Å: Chain A: L.31, D.304 Chain B: V.456, P.457, F.460, I.881, L.889 Ligands: LMT.1 Ligand excluded by PLIP LMT.37: 12 residues within 4Å: Chain C: V.454, M.458, F.564, K.565, G.569, F.883, V.911, N.929, Q.934, L.937, C.945 Ligands: LMT.47 Ligand excluded by PLIP LMT.38: 14 residues within 4Å: Chain B: R.10, F.13, V.16 Chain C: M.1, F.3, G.442, A.446, V.893, A.896, L.897, E.899, R.956, E.957 Ligands: LMT.39 Ligand excluded by PLIP LMT.39: 15 residues within 4Å: Chain B: D.9, R.10, P.11, I.12, A.15, I.19, F.22, I.373, V.377, L.494, L.497 Chain C: E.899, W.901 Ligands: LMT.38, GOL.52 Ligand excluded by PLIP LMT.40: 12 residues within 4Å: Chain A: E.899, W.901 Chain C: D.9, R.10, P.11, I.12, A.15, I.19, V.377, L.497 Ligands: LMT.2, PTY.12 Ligand excluded by PLIP LMT.41: 19 residues within 4Å: Chain C: E.36, Y.37, F.335, D.338, S.339, A.342, T.395, F.399, V.402, G.406, Q.575, K.577, A.986, F.987, L.994, G.1001, V.1004, R.1005, T.1008 Ligand excluded by PLIP LMT.42: 10 residues within 4Å: Chain C: P.38, D.39, L.389, G.390, F.391, K.470, Q.471, V.474, I.478, V.481 Ligand excluded by PLIP LMT.43: 22 residues within 4Å: Chain C: K.81, T.93, L.138, P.329, Y.330, Y.579, I.581, V.616, A.623, L.624, Q.625, F.626, F.636, G.638, P.674, I.676, L.677, G.678, L.679, G.680, D.867 Ligands: LMT.44 Ligand excluded by PLIP LMT.44: 15 residues within 4Å: Chain C: Q.46, R.48, Q.134, R.157, Q.176, Q.178, I.179, F.180, G.181, L.280, F.295, F.618, F.626, N.628 Ligands: LMT.43 Ligand excluded by PLIP LMT.45: 6 residues within 4Å: Chain A: F.460 Chain C: P.33, Y.387, G.390 Ligands: LMT.9, PTY.49 Ligand excluded by PLIP LMT.46: 13 residues within 4Å: Chain C: I.29, V.34, N.301, I.303, D.304, N.307, R.337, I.340, V.343, L.347, V.380, F.383, L.393 Ligand excluded by PLIP LMT.47: 17 residues within 4Å: Chain C: F.455, M.458, L.461, Y.469, A.473, G.570, F.571, G.682, S.842, Q.872, Q.875, N.877, F.883, Q.934, V.935, V.938 Ligands: LMT.37 Ligand excluded by PLIP LMT.48: 15 residues within 4Å: Chain B: D.166, R.170, P.172 Chain C: E.68, E.69, N.72, M.77, M.78, M.80, R.97, R.822, N.824, G.825, F.870, T.874 Ligand excluded by PLIP

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.12: 8 residues within 4Å: Chain A: L.888, F.891, W.901, L.1037, V.1038, R.1040 Chain C: I.19 Ligands: LMT.40 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.888, A:L.888, A:F.891, A:W.901, A:W.901, A:W.901, C:I.19 Salt bridges: A:R.1040 PTY.32: 8 residues within 4Å: Chain A: I.19, L.497 Chain B: F.891, W.901, R.1035, V.1038, T.1039 Ligands: LMT.3 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.891, B:W.901, B:W.901, A:I.19, A:L.497 Hydrogen bonds: B:R.1035, B:R.1035 PTY.33: 8 residues within 4Å: Chain B: L.20, I.27, P.30, L.31 Chain C: P.457, F.460, V.882, L.889 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:P.457, C:F.460, C:F.460, C:V.882, C:L.889, B:L.20, B:I.27, B:L.31 Hydrogen bonds: B:P.30 PTY.49: 15 residues within 4Å: Chain A: L.449, C.452, A.453, V.456, P.457, F.460, T.878, I.881, L.889 Chain C: L.31, N.301, D.304, Y.387, L.388 Ligands: LMT.45 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:V.456, A:P.457, A:F.460, A:F.460, A:F.460, A:T.878, A:I.881, A:L.889, C:L.31, C:L.31, C:Y.387, C:L.388 Hydrogen bonds: C:D.304 Water bridges: C:P.30, C:N.301, C:N.301

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: R.310, A.314, W.326 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: P.172, G.173, A.300, N.301, D.304, L.305 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: S.702, N.705, A.706 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain A: V.584, L.621, N.622, A.623, T.632, G.633, T.634, F.669 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain A: L.162, D.166, R.170, R.771 Chain B: N.824, G.825, Y.826 Ligands: LMT.10 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain A: A.118, R.119, L.120, R.125 Chain C: Q.216, R.242, N.764, D.765 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain A: R.157, S.182, G.183, E.184, G.276, S.277, R.774 Ligands: LMT.5 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain A: Q.216, R.242, Y.762, N.764, D.765 Chain B: R.119, L.120, P.121 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: A.198, R.199, K.255, A.257, Q.258, V.263 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain B: Q.435, R.438, E.957, Q.961 Ligands: LMT.25 Ligand excluded by PLIP GOL.35: 2 residues within 4Å: Chain B: K.963, E.967 Ligand excluded by PLIP GOL.36: 2 residues within 4Å: Chain B: Q.258, D.259 Ligand excluded by PLIP GOL.50: 5 residues within 4Å: Chain C: R.310, W.326, A.327, A.328, Y.614 Ligand excluded by PLIP GOL.51: 3 residues within 4Å: Chain C: E.246, R.270, I.271 Ligand excluded by PLIP GOL.52: 6 residues within 4Å: Chain C: R.956, E.959, I.960, Y.1031, R.1035 Ligands: LMT.39 Ligand excluded by PLIP GOL.53: 3 residues within 4Å: Chain C: G.696, Y.697, G.698 Ligand excluded by PLIP GOL.54: 6 residues within 4Å: Chain C: V.704, S.708, F.719, P.720, S.722, L.831 Ligand excluded by PLIP GOL.55: 1 residues within 4Å: Chain C: N.525 Ligand excluded by PLIP GOL.56: 6 residues within 4Å: Chain C: E.439, F.954, E.957, L.958, Q.961, L.975 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bharatham, N. et al., Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae. Nat Commun (2021)

Release Date

2021-09-22

Peptides

Efflux pump membrane transporter: 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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Efflux pump membrane transporter

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