SMTL ID : 2y1k.1

STRUCTURE OF HUMAN BUTYRYLCHOLINESTERASE INHIBITED BY CBDP (12H SOAK): PHOSPHOSERINE ADDUCT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-octamer

Ligands

8 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 6 residues within 4Å: Chain A: G.336, F.337, S.338, N.341, N.342 Ligands: NAG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.338, A:S.338 Hydrophobic interactions: A:N.341 Water bridges: A:G.336 NAG-FUC.19: 6 residues within 4Å: Chain B: G.336, F.337, S.338, N.341, N.342 Ligands: NAG.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.338, B:S.338 Hydrophobic interactions: B:N.341 Water bridges: B:G.336 NAG-FUC.37: 6 residues within 4Å: Chain C: G.336, F.337, S.338, N.341, N.342 Ligands: NAG.44 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.338, C:S.338 Hydrophobic interactions: C:N.341 Water bridges: C:G.336 NAG-FUC.55: 6 residues within 4Å: Chain D: G.336, F.337, S.338, N.341, N.342 Ligands: NAG.62 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.338, D:S.338 Hydrophobic interactions: D:N.341 Water bridges: D:G.336 NAG-FUC.73: 6 residues within 4Å: Chain E: G.336, F.337, S.338, N.341, N.342 Ligands: NAG.80 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.338, E:S.338 Hydrophobic interactions: E:N.341 Water bridges: E:G.336 NAG-FUC.91: 6 residues within 4Å: Chain F: G.336, F.337, S.338, N.341, N.342 Ligands: NAG.98 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.338, F:S.338 Hydrophobic interactions: F:N.341 Water bridges: F:G.336 NAG-FUC.109: 6 residues within 4Å: Chain G: G.336, F.337, S.338, N.341, N.342 Ligands: NAG.116 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.338, G:S.338 Hydrophobic interactions: G:N.341 Water bridges: G:G.336 NAG-FUC.127: 6 residues within 4Å: Chain H: G.336, F.337, S.338, N.341, N.342 Ligands: NAG.134 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.338, H:S.338 Hydrophobic interactions: H:N.341 Water bridges: H:G.336

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

SO4.2: 2 residues within 4Å: Chain A: R.347, Q.351 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: Q.316, G.413, N.414, N.415 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: W.231, R.242, L.286, S.287, V.288 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: K.323, Y.420, R.515 Chain H: R.509 Ligands: SO4.10 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: L.514, R.515, Q.518 Chain H: R.509 Ligands: SO4.9 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: R.347, Q.351 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: Q.316, G.413, N.414, N.415 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain B: W.231, R.242, L.286, S.287, V.288 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain B: K.323, Y.420, R.515 Chain F: R.509 Ligands: SO4.28 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain B: L.514, R.515, Q.518 Chain F: R.509 Ligands: SO4.27 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain C: R.347, Q.351 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain C: Q.316, G.413, N.414, N.415 Ligand excluded by PLIP SO4.43: 5 residues within 4Å: Chain C: W.231, R.242, L.286, S.287, V.288 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain C: K.323, Y.420, R.515 Chain E: R.509 Ligands: SO4.46 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain C: L.514, R.515, Q.518 Chain E: R.509 Ligands: SO4.45 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain D: R.347, Q.351 Ligand excluded by PLIP SO4.60: 4 residues within 4Å: Chain D: Q.316, G.413, N.414, N.415 Ligand excluded by PLIP SO4.61: 5 residues within 4Å: Chain D: W.231, R.242, L.286, S.287, V.288 Ligand excluded by PLIP SO4.63: 5 residues within 4Å: Chain D: K.323, Y.420, R.515 Chain G: R.509 Ligands: SO4.64 Ligand excluded by PLIP SO4.64: 5 residues within 4Å: Chain D: L.514, R.515, Q.518 Chain G: R.509 Ligands: SO4.63 Ligand excluded by PLIP SO4.74: 2 residues within 4Å: Chain E: R.347, Q.351 Ligand excluded by PLIP SO4.78: 4 residues within 4Å: Chain E: Q.316, G.413, N.414, N.415 Ligand excluded by PLIP SO4.79: 5 residues within 4Å: Chain E: W.231, R.242, L.286, S.287, V.288 Ligand excluded by PLIP SO4.81: 5 residues within 4Å: Chain C: R.509 Chain E: K.323, Y.420, R.515 Ligands: SO4.82 Ligand excluded by PLIP SO4.82: 5 residues within 4Å: Chain C: R.509 Chain E: L.514, R.515, Q.518 Ligands: SO4.81 Ligand excluded by PLIP SO4.92: 2 residues within 4Å: Chain F: R.347, Q.351 Ligand excluded by PLIP SO4.96: 4 residues within 4Å: Chain F: Q.316, G.413, N.414, N.415 Ligand excluded by PLIP SO4.97: 5 residues within 4Å: Chain F: W.231, R.242, L.286, S.287, V.288 Ligand excluded by PLIP SO4.99: 5 residues within 4Å: Chain B: R.509 Chain F: K.323, Y.420, R.515 Ligands: SO4.100 Ligand excluded by PLIP SO4.100: 5 residues within 4Å: Chain B: R.509 Chain F: L.514, R.515, Q.518 Ligands: SO4.99 Ligand excluded by PLIP SO4.110: 2 residues within 4Å: Chain G: R.347, Q.351 Ligand excluded by PLIP SO4.114: 4 residues within 4Å: Chain G: Q.316, G.413, N.414, N.415 Ligand excluded by PLIP SO4.115: 5 residues within 4Å: Chain G: W.231, R.242, L.286, S.287, V.288 Ligand excluded by PLIP SO4.117: 5 residues within 4Å: Chain D: R.509 Chain G: K.323, Y.420, R.515 Ligands: SO4.118 Ligand excluded by PLIP SO4.118: 5 residues within 4Å: Chain D: R.509 Chain G: L.514, R.515, Q.518 Ligands: SO4.117 Ligand excluded by PLIP SO4.128: 2 residues within 4Å: Chain H: R.347, Q.351 Ligand excluded by PLIP SO4.132: 4 residues within 4Å: Chain H: Q.316, G.413, N.414, N.415 Ligand excluded by PLIP SO4.133: 5 residues within 4Å: Chain H: W.231, R.242, L.286, S.287, V.288 Ligand excluded by PLIP SO4.135: 5 residues within 4Å: Chain A: R.509 Chain H: K.323, Y.420, R.515 Ligands: SO4.136 Ligand excluded by PLIP SO4.136: 5 residues within 4Å: Chain A: R.509 Chain H: L.514, R.515, Q.518 Ligands: SO4.135 Ligand excluded by PLIP

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

NA.3: 3 residues within 4Å: Chain A: F.525 Chain C: F.521, F.525 No protein-ligand interaction detected (PLIP) NA.21: 3 residues within 4Å: Chain B: F.525 Chain D: F.521, F.525 No protein-ligand interaction detected (PLIP) NA.39: 3 residues within 4Å: Chain A: F.521, F.525 Chain C: F.525 No protein-ligand interaction detected (PLIP) NA.57: 3 residues within 4Å: Chain B: F.521, F.525 Chain D: F.525 No protein-ligand interaction detected (PLIP) NA.75: 3 residues within 4Å: Chain E: F.525 Chain G: F.521, F.525 No protein-ligand interaction detected (PLIP) NA.93: 3 residues within 4Å: Chain F: F.525 Chain H: F.521, F.525 No protein-ligand interaction detected (PLIP) NA.111: 3 residues within 4Å: Chain E: F.521, F.525 Chain G: F.525 No protein-ligand interaction detected (PLIP) NA.129: 3 residues within 4Å: Chain F: F.521, F.525 Chain H: F.525 No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: S.487, T.488, T.508 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: S.487, T.488, T.508 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain C: S.487, T.488, T.508 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain D: S.487, T.488, T.508 Ligand excluded by PLIP CL.76: 3 residues within 4Å: Chain E: S.487, T.488, T.508 Ligand excluded by PLIP CL.94: 3 residues within 4Å: Chain F: S.487, T.488, T.508 Ligand excluded by PLIP CL.112: 3 residues within 4Å: Chain G: S.487, T.488, T.508 Ligand excluded by PLIP CL.130: 3 residues within 4Å: Chain H: S.487, T.488, T.508 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: M.16, L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.98, A:K.131 GOL.23: 6 residues within 4Å: Chain B: M.16, L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.98, B:K.131 GOL.41: 6 residues within 4Å: Chain C: M.16, L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.98, C:K.131 GOL.59: 6 residues within 4Å: Chain D: M.16, L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.98, D:K.131 GOL.77: 6 residues within 4Å: Chain E: M.16, L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:W.98, E:K.131 GOL.95: 6 residues within 4Å: Chain F: M.16, L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:W.98, F:K.131 GOL.113: 6 residues within 4Å: Chain G: M.16, L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:W.98, G:K.131 GOL.131: 6 residues within 4Å: Chain H: M.16, L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:W.98, H:K.131

56 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Non-covalent)

NAG.8: 1 residues within 4Å: Ligands: NAG-FUC.1 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.106, N.188, K.190 Ligands: FUC.12 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: R.14, N.57 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.256, T.258 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: Y.237, N.241, N.245 Ligands: NAG.17 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: K.248 Ligands: NAG.16, FUC.18 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Ligands: NAG-FUC.19 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.106, N.188, K.190 Ligands: FUC.30 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: R.14, N.57 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: R.465, K.469, E.482, N.485 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.256, T.258 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: Y.237, N.241, N.245 Ligands: NAG.35 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: K.248 Ligands: NAG.34, FUC.36 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Ligands: NAG-FUC.37 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: N.106, N.188, K.190 Ligands: FUC.48 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: R.14, N.57 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: R.465, K.469, E.482, N.485 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.256, T.258 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: Y.237, N.241, N.245 Ligands: NAG.53 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: K.248 Ligands: NAG.52, FUC.54 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Ligands: NAG-FUC.55 Ligand excluded by PLIP NAG.65: 4 residues within 4Å: Chain D: N.106, N.188, K.190 Ligands: FUC.66 Ligand excluded by PLIP NAG.67: 2 residues within 4Å: Chain D: R.14, N.57 Ligand excluded by PLIP NAG.68: 4 residues within 4Å: Chain D: R.465, K.469, E.482, N.485 Ligand excluded by PLIP NAG.69: 2 residues within 4Å: Chain D: N.256, T.258 Ligand excluded by PLIP NAG.70: 4 residues within 4Å: Chain D: Y.237, N.241, N.245 Ligands: NAG.71 Ligand excluded by PLIP NAG.71: 3 residues within 4Å: Chain D: K.248 Ligands: NAG.70, FUC.72 Ligand excluded by PLIP NAG.80: 1 residues within 4Å: Ligands: NAG-FUC.73 Ligand excluded by PLIP NAG.83: 4 residues within 4Å: Chain E: N.106, N.188, K.190 Ligands: FUC.84 Ligand excluded by PLIP NAG.85: 2 residues within 4Å: Chain E: R.14, N.57 Ligand excluded by PLIP NAG.86: 4 residues within 4Å: Chain E: R.465, K.469, E.482, N.485 Ligand excluded by PLIP NAG.87: 2 residues within 4Å: Chain E: N.256, T.258 Ligand excluded by PLIP NAG.88: 4 residues within 4Å: Chain E: Y.237, N.241, N.245 Ligands: NAG.89 Ligand excluded by PLIP NAG.89: 3 residues within 4Å: Chain E: K.248 Ligands: NAG.88, FUC.90 Ligand excluded by PLIP NAG.98: 1 residues within 4Å: Ligands: NAG-FUC.91 Ligand excluded by PLIP NAG.101: 4 residues within 4Å: Chain F: N.106, N.188, K.190 Ligands: FUC.102 Ligand excluded by PLIP NAG.103: 2 residues within 4Å: Chain F: R.14, N.57 Ligand excluded by PLIP NAG.104: 4 residues within 4Å: Chain F: R.465, K.469, E.482, N.485 Ligand excluded by PLIP NAG.105: 2 residues within 4Å: Chain F: N.256, T.258 Ligand excluded by PLIP NAG.106: 4 residues within 4Å: Chain F: Y.237, N.241, N.245 Ligands: NAG.107 Ligand excluded by PLIP NAG.107: 3 residues within 4Å: Chain F: K.248 Ligands: NAG.106, FUC.108 Ligand excluded by PLIP NAG.116: 1 residues within 4Å: Ligands: NAG-FUC.109 Ligand excluded by PLIP NAG.119: 4 residues within 4Å: Chain G: N.106, N.188, K.190 Ligands: FUC.120 Ligand excluded by PLIP NAG.121: 2 residues within 4Å: Chain G: R.14, N.57 Ligand excluded by PLIP NAG.122: 4 residues within 4Å: Chain G: R.465, K.469, E.482, N.485 Ligand excluded by PLIP NAG.123: 2 residues within 4Å: Chain G: N.256, T.258 Ligand excluded by PLIP NAG.124: 4 residues within 4Å: Chain G: Y.237, N.241, N.245 Ligands: NAG.125 Ligand excluded by PLIP NAG.125: 3 residues within 4Å: Chain G: K.248 Ligands: NAG.124, FUC.126 Ligand excluded by PLIP NAG.134: 1 residues within 4Å: Ligands: NAG-FUC.127 Ligand excluded by PLIP NAG.137: 4 residues within 4Å: Chain H: N.106, N.188, K.190 Ligands: FUC.138 Ligand excluded by PLIP NAG.139: 2 residues within 4Å: Chain H: R.14, N.57 Ligand excluded by PLIP NAG.140: 4 residues within 4Å: Chain H: R.465, K.469, E.482, N.485 Ligand excluded by PLIP NAG.141: 2 residues within 4Å: Chain H: N.256, T.258 Ligand excluded by PLIP NAG.142: 4 residues within 4Å: Chain H: Y.237, N.241, N.245 Ligands: NAG.143 Ligand excluded by PLIP NAG.143: 3 residues within 4Å: Chain H: K.248 Ligands: NAG.142, FUC.144 Ligand excluded by PLIP

16 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.12: 6 residues within 4Å: Chain A: N.188, K.190, S.191, R.219, K.476 Ligands: NAG.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.188, A:S.191, A:R.219 Water bridges: A:T.108, A:S.191, A:S.191 FUC.18: 5 residues within 4Å: Chain A: N.245, K.248, F.278, V.280 Ligands: NAG.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.245 Hydrogen bonds: A:K.248, A:F.278 FUC.30: 6 residues within 4Å: Chain B: N.188, K.190, S.191, R.219, K.476 Ligands: NAG.29 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.188, B:S.191, B:R.219 Water bridges: B:S.191, B:S.191 FUC.36: 5 residues within 4Å: Chain B: N.245, K.248, F.278, V.280 Ligands: NAG.35 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.245 Hydrogen bonds: B:K.248, B:F.278 FUC.48: 6 residues within 4Å: Chain C: N.188, K.190, S.191, R.219, K.476 Ligands: NAG.47 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.188, C:S.191, C:R.219 Water bridges: C:S.191, C:S.191 FUC.54: 5 residues within 4Å: Chain C: N.245, K.248, F.278, V.280 Ligands: NAG.53 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.245 Hydrogen bonds: C:K.248, C:F.278 FUC.66: 6 residues within 4Å: Chain D: N.188, K.190, S.191, R.219, K.476 Ligands: NAG.65 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.188, D:S.191, D:R.219 Water bridges: D:T.108, D:S.191, D:S.191 FUC.72: 5 residues within 4Å: Chain D: N.245, K.248, F.278, V.280 Ligands: NAG.71 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:N.245 Hydrogen bonds: D:K.248, D:F.278 FUC.84: 6 residues within 4Å: Chain E: N.188, K.190, S.191, R.219, K.476 Ligands: NAG.83 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.188, E:S.191, E:R.219 Water bridges: E:T.108, E:S.191, E:S.191 FUC.90: 5 residues within 4Å: Chain E: N.245, K.248, F.278, V.280 Ligands: NAG.89 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:N.245 Hydrogen bonds: E:K.248, E:F.278 FUC.102: 6 residues within 4Å: Chain F: N.188, K.190, S.191, R.219, K.476 Ligands: NAG.101 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.188, F:S.191, F:R.219 Water bridges: F:T.108, F:S.191, F:S.191 FUC.108: 5 residues within 4Å: Chain F: N.245, K.248, F.278, V.280 Ligands: NAG.107 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:N.245 Hydrogen bonds: F:K.248, F:F.278 FUC.120: 6 residues within 4Å: Chain G: N.188, K.190, S.191, R.219, K.476 Ligands: NAG.119 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:N.188, G:S.191, G:R.219 Water bridges: G:S.191, G:S.191 FUC.126: 5 residues within 4Å: Chain G: N.245, K.248, F.278, V.280 Ligands: NAG.125 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:N.245 Hydrogen bonds: G:K.248, G:F.278 FUC.138: 6 residues within 4Å: Chain H: N.188, K.190, S.191, R.219, K.476 Ligands: NAG.137 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:N.188, H:S.191, H:R.219 Water bridges: H:S.191, H:S.191 FUC.144: 5 residues within 4Å: Chain H: N.245, K.248, F.278, V.280 Ligands: NAG.143 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:N.245 Hydrogen bonds: H:K.248, H:F.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carletti, E. et al., Reaction of Cresyl Saligenin Phosphate, the Organophosphorus Agent Implicated in Aerotoxic Syndrome, with Human Cholinesterases: Mechanistic Studies Employing Kinetics, Mass Spectrometry, and X-Ray Structure Analysis. Chem.Res.Toxicol. (2011)

Release Date

2011-06-29

Peptides

CHOLINESTERASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

CHOLINESTERASE

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