SMTL ID : 4b0o.1

Crystal structure of soman-aged human butyrylcholinesterase in complex with benzyl pyridinium-4-methyltrichloroacetimidate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-octamer

Ligands

16 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG-FUL.1: 7 residues within 4Å: Chain A: E.238, N.241, N.245, K.248, L.249, F.278, P.281 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.248, A:L.249 Hydrogen bonds: A:K.248 NAG-NAG-FUL.2: 6 residues within 4Å: Chain A: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.336 NAG-NAG-FUL.19: 7 residues within 4Å: Chain B: E.238, N.241, N.245, K.248, L.249, F.278, P.281 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.248, B:L.249 Hydrogen bonds: B:K.248 NAG-NAG-FUL.20: 6 residues within 4Å: Chain B: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.336 NAG-NAG-FUL.37: 7 residues within 4Å: Chain C: E.238, N.241, N.245, K.248, L.249, F.278, P.281 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.248, C:L.249 Hydrogen bonds: C:K.248 NAG-NAG-FUL.38: 6 residues within 4Å: Chain C: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.336 NAG-NAG-FUL.55: 7 residues within 4Å: Chain D: E.238, N.241, N.245, K.248, L.249, F.278, P.281 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:K.248, D:L.249 Hydrogen bonds: D:K.248 NAG-NAG-FUL.56: 6 residues within 4Å: Chain D: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.336 NAG-NAG-FUL.73: 7 residues within 4Å: Chain E: E.238, N.241, N.245, K.248, L.249, F.278, P.281 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:K.248, E:L.249 Hydrogen bonds: E:K.248 NAG-NAG-FUL.74: 6 residues within 4Å: Chain E: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.336 NAG-NAG-FUL.91: 7 residues within 4Å: Chain F: E.238, N.241, N.245, K.248, L.249, F.278, P.281 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:K.248, F:L.249 Hydrogen bonds: F:K.248 NAG-NAG-FUL.92: 6 residues within 4Å: Chain F: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.336 NAG-NAG-FUL.109: 7 residues within 4Å: Chain G: E.238, N.241, N.245, K.248, L.249, F.278, P.281 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:K.248, G:L.249 Hydrogen bonds: G:K.248 NAG-NAG-FUL.110: 6 residues within 4Å: Chain G: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.336 NAG-NAG-FUL.127: 7 residues within 4Å: Chain H: E.238, N.241, N.245, K.248, L.249, F.278, P.281 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:K.248, H:L.249 Hydrogen bonds: H:K.248 NAG-NAG-FUL.128: 6 residues within 4Å: Chain H: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.336

8 x GLY: GLYCINE(Non-covalent)

GLY.3: 5 residues within 4Å: Chain A: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.98 Salt bridges: A:K.131 GLY.21: 5 residues within 4Å: Chain B: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.98 Salt bridges: B:K.131 GLY.39: 5 residues within 4Å: Chain C: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.98 Salt bridges: C:K.131 GLY.57: 5 residues within 4Å: Chain D: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.98 Salt bridges: D:K.131 GLY.75: 5 residues within 4Å: Chain E: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:W.98 Salt bridges: E:K.131 GLY.93: 5 residues within 4Å: Chain F: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:W.98 Salt bridges: F:K.131 GLY.111: 5 residues within 4Å: Chain G: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:W.98 Salt bridges: G:K.131 GLY.129: 5 residues within 4Å: Chain H: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:W.98 Salt bridges: H:K.131

32 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 2 residues within 4Å: Chain A: R.14, N.57 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.106, N.188, K.190 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: R.465, K.469, N.485 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.256 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: R.14, N.57 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.106, N.188, K.190 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: R.465, K.469, N.485 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.256 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: R.14, N.57 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.106, N.188, K.190 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: R.465, K.469, N.485 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.256 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain D: R.14, N.57 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain D: N.106, N.188, K.190 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain D: R.465, K.469, N.485 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain D: N.256 Ligand excluded by PLIP NAG.76: 2 residues within 4Å: Chain E: R.14, N.57 Ligand excluded by PLIP NAG.77: 3 residues within 4Å: Chain E: N.106, N.188, K.190 Ligand excluded by PLIP NAG.78: 3 residues within 4Å: Chain E: R.465, K.469, N.485 Ligand excluded by PLIP NAG.79: 1 residues within 4Å: Chain E: N.256 Ligand excluded by PLIP NAG.94: 2 residues within 4Å: Chain F: R.14, N.57 Ligand excluded by PLIP NAG.95: 3 residues within 4Å: Chain F: N.106, N.188, K.190 Ligand excluded by PLIP NAG.96: 3 residues within 4Å: Chain F: R.465, K.469, N.485 Ligand excluded by PLIP NAG.97: 1 residues within 4Å: Chain F: N.256 Ligand excluded by PLIP NAG.112: 2 residues within 4Å: Chain G: R.14, N.57 Ligand excluded by PLIP NAG.113: 3 residues within 4Å: Chain G: N.106, N.188, K.190 Ligand excluded by PLIP NAG.114: 3 residues within 4Å: Chain G: R.465, K.469, N.485 Ligand excluded by PLIP NAG.115: 1 residues within 4Å: Chain G: N.256 Ligand excluded by PLIP NAG.130: 2 residues within 4Å: Chain H: R.14, N.57 Ligand excluded by PLIP NAG.131: 3 residues within 4Å: Chain H: N.106, N.188, K.190 Ligand excluded by PLIP NAG.132: 3 residues within 4Å: Chain H: R.465, K.469, N.485 Ligand excluded by PLIP NAG.133: 1 residues within 4Å: Chain H: N.256 Ligand excluded by PLIP

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

CL.8: 1 residues within 4Å: Chain A: R.347 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: T.512 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: R.40 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: P.189, F.217, T.218 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: Q.316, N.415 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain B: R.347 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: T.512 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: R.40 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: P.189, F.217, T.218 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: Q.316, N.415 Ligand excluded by PLIP CL.44: 1 residues within 4Å: Chain C: R.347 Ligand excluded by PLIP CL.45: 1 residues within 4Å: Chain C: T.512 Ligand excluded by PLIP CL.46: 1 residues within 4Å: Chain C: R.40 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Chain C: P.189, F.217, T.218 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain C: Q.316, N.415 Ligand excluded by PLIP CL.62: 1 residues within 4Å: Chain D: R.347 Ligand excluded by PLIP CL.63: 1 residues within 4Å: Chain D: T.512 Ligand excluded by PLIP CL.64: 1 residues within 4Å: Chain D: R.40 Ligand excluded by PLIP CL.65: 3 residues within 4Å: Chain D: P.189, F.217, T.218 Ligand excluded by PLIP CL.66: 2 residues within 4Å: Chain D: Q.316, N.415 Ligand excluded by PLIP CL.80: 1 residues within 4Å: Chain E: R.347 Ligand excluded by PLIP CL.81: 1 residues within 4Å: Chain E: T.512 Ligand excluded by PLIP CL.82: 1 residues within 4Å: Chain E: R.40 Ligand excluded by PLIP CL.83: 3 residues within 4Å: Chain E: P.189, F.217, T.218 Ligand excluded by PLIP CL.84: 2 residues within 4Å: Chain E: Q.316, N.415 Ligand excluded by PLIP CL.98: 1 residues within 4Å: Chain F: R.347 Ligand excluded by PLIP CL.99: 1 residues within 4Å: Chain F: T.512 Ligand excluded by PLIP CL.100: 1 residues within 4Å: Chain F: R.40 Ligand excluded by PLIP CL.101: 3 residues within 4Å: Chain F: P.189, F.217, T.218 Ligand excluded by PLIP CL.102: 2 residues within 4Å: Chain F: Q.316, N.415 Ligand excluded by PLIP CL.116: 1 residues within 4Å: Chain G: R.347 Ligand excluded by PLIP CL.117: 1 residues within 4Å: Chain G: T.512 Ligand excluded by PLIP CL.118: 1 residues within 4Å: Chain G: R.40 Ligand excluded by PLIP CL.119: 3 residues within 4Å: Chain G: P.189, F.217, T.218 Ligand excluded by PLIP CL.120: 2 residues within 4Å: Chain G: Q.316, N.415 Ligand excluded by PLIP CL.134: 1 residues within 4Å: Chain H: R.347 Ligand excluded by PLIP CL.135: 1 residues within 4Å: Chain H: T.512 Ligand excluded by PLIP CL.136: 1 residues within 4Å: Chain H: R.40 Ligand excluded by PLIP CL.137: 3 residues within 4Å: Chain H: P.189, F.217, T.218 Ligand excluded by PLIP CL.138: 2 residues within 4Å: Chain H: Q.316, N.415 Ligand excluded by PLIP

8 x BR: BROMIDE ION(Non-covalent)

BR.13: 3 residues within 4Å: Chain A: E.197, X.198 Ligands: 15F.18 Ligand excluded by PLIP BR.31: 3 residues within 4Å: Chain B: E.197, X.198 Ligands: 15F.36 Ligand excluded by PLIP BR.49: 3 residues within 4Å: Chain C: E.197, X.198 Ligands: 15F.54 Ligand excluded by PLIP BR.67: 3 residues within 4Å: Chain D: E.197, X.198 Ligands: 15F.72 Ligand excluded by PLIP BR.85: 3 residues within 4Å: Chain E: E.197, X.198 Ligands: 15F.90 Ligand excluded by PLIP BR.103: 3 residues within 4Å: Chain F: E.197, X.198 Ligands: 15F.108 Ligand excluded by PLIP BR.121: 3 residues within 4Å: Chain G: E.197, X.198 Ligands: 15F.126 Ligand excluded by PLIP BR.139: 3 residues within 4Å: Chain H: E.197, X.198 Ligands: 15F.144 Ligand excluded by PLIP

16 x CA: CALCIUM ION(Non-covalent)

CA.14: 2 residues within 4Å: Chain A: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.15: 3 residues within 4Å: Chain A: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP) CA.32: 2 residues within 4Å: Chain B: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.33: 3 residues within 4Å: Chain B: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP) CA.50: 2 residues within 4Å: Chain C: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.51: 3 residues within 4Å: Chain C: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP) CA.68: 2 residues within 4Å: Chain D: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.69: 3 residues within 4Å: Chain D: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP) CA.86: 2 residues within 4Å: Chain E: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.87: 3 residues within 4Å: Chain E: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP) CA.104: 2 residues within 4Å: Chain F: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.105: 3 residues within 4Å: Chain F: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP) CA.122: 2 residues within 4Å: Chain G: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.123: 3 residues within 4Å: Chain G: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP) CA.140: 2 residues within 4Å: Chain H: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.141: 3 residues within 4Å: Chain H: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP)

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

NA.16: 1 residues within 4Å: Chain A: R.242 Ligand excluded by PLIP NA.17: 2 residues within 4Å: Chain A: C.66, Q.270 Ligand excluded by PLIP NA.34: 1 residues within 4Å: Chain B: R.242 Ligand excluded by PLIP NA.35: 2 residues within 4Å: Chain B: C.66, Q.270 Ligand excluded by PLIP NA.52: 1 residues within 4Å: Chain C: R.242 Ligand excluded by PLIP NA.53: 2 residues within 4Å: Chain C: C.66, Q.270 Ligand excluded by PLIP NA.70: 1 residues within 4Å: Chain D: R.242 Ligand excluded by PLIP NA.71: 2 residues within 4Å: Chain D: C.66, Q.270 Ligand excluded by PLIP NA.88: 1 residues within 4Å: Chain E: R.242 Ligand excluded by PLIP NA.89: 2 residues within 4Å: Chain E: C.66, Q.270 Ligand excluded by PLIP NA.106: 1 residues within 4Å: Chain F: R.242 Ligand excluded by PLIP NA.107: 2 residues within 4Å: Chain F: C.66, Q.270 Ligand excluded by PLIP NA.124: 1 residues within 4Å: Chain G: R.242 Ligand excluded by PLIP NA.125: 2 residues within 4Å: Chain G: C.66, Q.270 Ligand excluded by PLIP NA.142: 1 residues within 4Å: Chain H: R.242 Ligand excluded by PLIP NA.143: 2 residues within 4Å: Chain H: C.66, Q.270 Ligand excluded by PLIP

8 x 15F: 1-BENZYL-4-({[(1E)-2,2,2-TRICHLOROETHANIMIDOYL]OXY}METHYL)PYRIDINIUM(Non-covalent)

15F.18: 14 residues within 4Å: Chain A: D.70, W.82, G.116, G.117, P.285, L.286, S.287, A.328, F.329, W.430, M.437, H.438, Y.440 Ligands: BR.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.328, A:F.329, A:W.430, A:Y.440 pi-Stacking: A:W.82, A:Y.332 Halogen bonds: A:S.287 15F.36: 14 residues within 4Å: Chain B: D.70, W.82, G.116, G.117, P.285, L.286, S.287, A.328, F.329, W.430, M.437, H.438, Y.440 Ligands: BR.31 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.328, B:F.329, B:W.430, B:Y.440 pi-Stacking: B:W.82, B:Y.332 Halogen bonds: B:S.287 15F.54: 14 residues within 4Å: Chain C: D.70, W.82, G.116, G.117, P.285, L.286, S.287, A.328, F.329, W.430, M.437, H.438, Y.440 Ligands: BR.49 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.328, C:F.329, C:W.430, C:Y.440 pi-Stacking: C:W.82, C:Y.332 Halogen bonds: C:S.287 15F.72: 14 residues within 4Å: Chain D: D.70, W.82, G.116, G.117, P.285, L.286, S.287, A.328, F.329, W.430, M.437, H.438, Y.440 Ligands: BR.67 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.328, D:F.329, D:W.430, D:Y.440 pi-Stacking: D:W.82, D:Y.332 Halogen bonds: D:S.287 15F.90: 14 residues within 4Å: Chain E: D.70, W.82, G.116, G.117, P.285, L.286, S.287, A.328, F.329, W.430, M.437, H.438, Y.440 Ligands: BR.85 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:A.328, E:F.329, E:W.430, E:Y.440 pi-Stacking: E:W.82, E:Y.332 Halogen bonds: E:S.287 15F.108: 14 residues within 4Å: Chain F: D.70, W.82, G.116, G.117, P.285, L.286, S.287, A.328, F.329, W.430, M.437, H.438, Y.440 Ligands: BR.103 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:A.328, F:F.329, F:W.430, F:Y.440 pi-Stacking: F:W.82, F:Y.332 Halogen bonds: F:S.287 15F.126: 14 residues within 4Å: Chain G: D.70, W.82, G.116, G.117, P.285, L.286, S.287, A.328, F.329, W.430, M.437, H.438, Y.440 Ligands: BR.121 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:A.328, G:F.329, G:W.430, G:Y.440 pi-Stacking: G:W.82, G:Y.332 Halogen bonds: G:S.287 15F.144: 14 residues within 4Å: Chain H: D.70, W.82, G.116, G.117, P.285, L.286, S.287, A.328, F.329, W.430, M.437, H.438, Y.440 Ligands: BR.139 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:A.328, H:F.329, H:W.430, H:Y.440 pi-Stacking: H:W.82, H:Y.332 Halogen bonds: H:S.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wandhammer, M. et al., A Step Toward the Reactivation of Aged Cholinesterases -Crystal Structure of Ligands Binding to Aged Human Butyrylcholinesterase. Chem.Biol.Interact (2013)

Release Date

2012-08-29

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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