SMTL ID : 5t77.1

Crystal structure of the MOP flippase MurJ

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 7 residues within 4Å: Chain A: R.24, F.28, Y.41, F.42, I.45, I.165, R.255 Ligand excluded by PLIP CL.2: 7 residues within 4Å: Chain A: L.67, K.71, F.79, H.210, H.213 Ligands: CL.3, ZN.6 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: K.71, H.210, H.213 Ligands: CL.2, ZN.6 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: S.72, G.73, K.76 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: S.35, Y.36, K.244 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: K.71, H.210, H.213 Ligands: CL.2, CL.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.210, A:H.213

3 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: E.74, D.77, H.202, K.203 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.74, A:D.77, H2O.3, H2O.4, H2O.4 CA.8: 2 residues within 4Å: Chain A: V.34, S.35 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:V.34, H2O.2, H2O.3, H2O.5, H2O.5 CA.9: 3 residues within 4Å: Chain A: E.318, H.319 Ligands: OLC.33 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.318, H2O.1, H2O.3, H2O.4, H2O.6

2 x NA: SODIUM ION(Non-functional Binders)

NA.10: 2 residues within 4Å: Chain A: F.241, Y.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.242 NA.11: 2 residues within 4Å: Chain A: S.35 Ligands: 1PE.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.35, A:S.35

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.12: 9 residues within 4Å: Chain A: Y.285, N.288, D.289, K.292, P.413, K.415, D.416, Y.462 Ligands: OLB.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.292, A:D.416 1PE.13: 12 residues within 4Å: Chain A: F.23, V.26, L.27, K.30, Y.31, F.170, H.319, G.320 Ligands: 1PE.14, OLC.33, OLC.36, OLC.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.30, A:Y.31, A:Y.31, A:G.320 1PE.14: 7 residues within 4Å: Chain A: K.30, Y.31, T.173, G.320, A.321 Ligands: NA.11, 1PE.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.30, A:A.321 Water bridges: A:F.32, A:A.321, A:A.321

7 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.15: 8 residues within 4Å: Chain A: N.107, L.108, A.111, V.233, V.234, N.237, F.241 Ligands: OLB.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.233 Hydrogen bonds: A:N.237 OLB.16: 20 residues within 4Å: Chain A: L.80, S.81, I.84, S.88, I.91, L.92, V.95, P.130, Y.133, F.134, L.137, F.192, F.193, I.196, I.199, I.200, H.202, K.203, Y.204 Ligands: OLB.19 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.92, A:Y.133, A:Y.133, A:Y.133, A:F.134 Hydrogen bonds: A:S.81, A:S.81 Water bridges: A:S.81 OLB.17: 14 residues within 4Å: Chain A: L.295, I.299, M.302, P.342, F.343, I.346, V.402, L.406, K.410, T.411, F.412, I.414, F.417 Ligands: OLC.45 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.342, A:P.342, A:F.343, A:F.343, A:I.346, A:F.412, A:F.412, A:F.417 Hydrogen bonds: A:T.411, A:T.411, A:F.412 OLB.18: 7 residues within 4Å: Chain A: V.234, N.237, V.238, F.241, I.379, L.383 Ligands: OLB.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.241 OLB.19: 10 residues within 4Å: Chain A: L.126, I.127, P.130, F.134, L.185, I.189 Ligands: OLB.16, OLC.32, OLC.43, OLC.44 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.130, A:L.185 OLB.20: 12 residues within 4Å: Chain A: D.289, K.292, T.293, F.296, I.420, L.455, S.458, S.459, Y.462, I.466 Ligands: 1PE.12, OLC.51 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.296, A:Y.462, A:Y.462 Hydrogen bonds: A:D.289, A:D.289, A:T.293, A:T.293 OLB.21: 15 residues within 4Å: Chain A: F.264, F.296, F.297, P.300, S.301, G.304, M.427, I.447, G.450, I.451, Y.454, L.455 Ligands: OLC.47, OLC.51, OLC.53 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.297, A:F.297, A:P.300, A:I.451, A:L.455

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

OLC.22: 18 residues within 4Å: Chain A: F.47, L.51, F.87, I.90, I.91, L.94, V.95, S.98, I.105, S.129, I.132, F.136, L.215, K.216, F.218, F.219, P.220, F.222 Ligand excluded by PLIP OLC.23: 8 residues within 4Å: Chain A: N.85, S.88, L.89, Y.204, F.206, T.207, I.208, K.209 Ligand excluded by PLIP OLC.24: 6 residues within 4Å: Chain A: Y.99, F.100, F.101, P.102, E.103, K.122 Ligand excluded by PLIP OLC.25: 12 residues within 4Å: Chain A: T.164, I.167, G.168, L.171, Y.175, I.178, S.179, I.182, G.183, I.186 Ligands: OLC.32, OLC.34 Ligand excluded by PLIP OLC.26: 3 residues within 4Å: Chain A: I.396, I.399, I.400 Ligand excluded by PLIP OLC.27: 11 residues within 4Å: Chain A: L.145, K.150, W.153, P.154, L.156, T.157, S.159, I.160, I.163, S.194, I.195 Ligand excluded by PLIP OLC.28: 9 residues within 4Å: Chain A: F.436, T.437, N.439, F.441, W.442, L.444, I.445, I.447, L.448 Ligand excluded by PLIP OLC.29: 11 residues within 4Å: Chain A: T.360, K.361, F.364, I.365, T.368, I.369, L.372 Ligands: OLC.39, OLC.41, OLC.42, OLC.52 Ligand excluded by PLIP OLC.30: 12 residues within 4Å: Chain A: T.224, V.227, S.228, I.230, F.364, A.367, T.368, S.371, L.372, I.375 Ligands: OLC.39, OLC.40 Ligand excluded by PLIP OLC.31: 7 residues within 4Å: Chain A: K.332, F.381, Y.385, I.388, G.389, L.392 Ligands: OLC.35 Ligand excluded by PLIP OLC.32: 11 residues within 4Å: Chain A: K.123, I.127, I.178, I.182, L.185, I.186, I.189 Ligands: OLB.19, OLC.25, OLC.34, OLC.44 Ligand excluded by PLIP OLC.33: 14 residues within 4Å: Chain A: F.15, F.16, I.19, L.22, F.23, V.26, F.315, F.316, H.319, E.440, F.441 Ligands: CA.9, 1PE.13, OLC.36 Ligand excluded by PLIP OLC.34: 4 residues within 4Å: Chain A: I.182, I.186 Ligands: OLC.25, OLC.32 Ligand excluded by PLIP OLC.35: 7 residues within 4Å: Chain A: K.332, I.335, A.336, L.339, I.388, L.392 Ligands: OLC.31 Ligand excluded by PLIP OLC.36: 6 residues within 4Å: Chain A: F.16, I.19, L.20, F.23 Ligands: 1PE.13, OLC.33 Ligand excluded by PLIP OLC.37: 4 residues within 4Å: Chain A: L.418, K.419, L.422 Ligands: OLC.38 Ligand excluded by PLIP OLC.38: 3 residues within 4Å: Chain A: L.418 Ligands: OLC.37, OLC.48 Ligand excluded by PLIP OLC.39: 6 residues within 4Å: Chain A: T.224, V.227, F.364 Ligands: OLC.29, OLC.30, OLC.41 Ligand excluded by PLIP OLC.40: 3 residues within 4Å: Chain A: T.368, L.372 Ligands: OLC.30 Ligand excluded by PLIP OLC.41: 3 residues within 4Å: Chain A: F.364 Ligands: OLC.29, OLC.39 Ligand excluded by PLIP OLC.42: 2 residues within 4Å: Ligands: OLC.29, OLC.52 Ligand excluded by PLIP OLC.43: 3 residues within 4Å: Chain A: Y.99, L.126 Ligands: OLB.19 Ligand excluded by PLIP OLC.44: 2 residues within 4Å: Ligands: OLB.19, OLC.32 Ligand excluded by PLIP OLC.45: 9 residues within 4Å: Chain A: M.302, V.303, I.306, F.307, I.335, L.339, F.343, L.428 Ligands: OLB.17 Ligand excluded by PLIP OLC.46: 3 residues within 4Å: Chain A: Y.31, F.170 Ligands: 1PE.13 Ligand excluded by PLIP OLC.47: 7 residues within 4Å: Chain A: L.263, F.264, V.268, F.297 Ligands: OLB.21, OLC.49, OLC.53 Ligand excluded by PLIP OLC.48: 4 residues within 4Å: Chain A: I.414, K.415, L.418 Ligands: OLC.38 Ligand excluded by PLIP OLC.49: 8 residues within 4Å: Chain A: S.11, T.14, F.15, L.263, S.267, V.268 Ligands: OLC.47, OLC.53 Ligand excluded by PLIP OLC.50: 8 residues within 4Å: Chain A: I.369, I.400, L.403, Y.404, F.407, S.408, K.410 Ligands: OLC.52 Ligand excluded by PLIP OLC.51: 6 residues within 4Å: Chain A: T.293, F.296, F.297 Ligands: OLB.20, OLB.21, OLC.53 Ligand excluded by PLIP OLC.52: 6 residues within 4Å: Chain A: I.365, I.369, Y.404 Ligands: OLC.29, OLC.42, OLC.50 Ligand excluded by PLIP OLC.53: 10 residues within 4Å: Chain A: V.268, S.269, V.271, V.272, T.293, F.297 Ligands: OLB.21, OLC.47, OLC.49, OLC.51 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuk, A.C. et al., Crystal structure of the MOP flippase MurJ in an inward-facing conformation. Nat. Struct. Mol. Biol. (2017)

Release Date

2016-12-28

Peptides

Putative lipid II flippase MurJ: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Putative lipid II flippase MurJ

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