SMTL ID : 2xqj.1

X-ray Structure of human butyrylcholinesterase inhibited by pure enantiomer VX-(R)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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

NAG-NAG-FUL.1: 6 residues within 4Å: Chain A: P.333, G.334, F.335, S.336, N.339, N.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.336, A:G.334 NAG-NAG-FUL.2: 8 residues within 4Å: Chain A: E.236, N.239, N.243, K.246, L.247, F.276, V.278, P.279 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.243, A:L.247 NAG-NAG-FUL.19: 6 residues within 4Å: Chain B: P.333, G.334, F.335, S.336, N.339, N.340 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.336, B:G.334 NAG-NAG-FUL.20: 8 residues within 4Å: Chain B: E.236, N.239, N.243, K.246, L.247, F.276, V.278, P.279 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.243, B:L.247 NAG-NAG-FUL.37: 6 residues within 4Å: Chain C: P.333, G.334, F.335, S.336, N.339, N.340 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.336, C:G.334 NAG-NAG-FUL.38: 8 residues within 4Å: Chain C: E.236, N.239, N.243, K.246, L.247, F.276, V.278, P.279 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.243, C:L.247 NAG-NAG-FUL.55: 6 residues within 4Å: Chain D: P.333, G.334, F.335, S.336, N.339, N.340 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.336, D:G.334 NAG-NAG-FUL.56: 8 residues within 4Å: Chain D: E.236, N.239, N.243, K.246, L.247, F.276, V.278, P.279 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.243, D:L.247 NAG-NAG-FUL.73: 6 residues within 4Å: Chain E: P.333, G.334, F.335, S.336, N.339, N.340 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.336, E:G.334 NAG-NAG-FUL.74: 8 residues within 4Å: Chain E: E.236, N.239, N.243, K.246, L.247, F.276, V.278, P.279 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:N.243, E:L.247 NAG-NAG-FUL.91: 6 residues within 4Å: Chain F: P.333, G.334, F.335, S.336, N.339, N.340 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.336, F:G.334 NAG-NAG-FUL.92: 8 residues within 4Å: Chain F: E.236, N.239, N.243, K.246, L.247, F.276, V.278, P.279 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:N.243, F:L.247 NAG-NAG-FUL.109: 6 residues within 4Å: Chain G: P.333, G.334, F.335, S.336, N.339, N.340 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.336, G:G.334 NAG-NAG-FUL.110: 8 residues within 4Å: Chain G: E.236, N.239, N.243, K.246, L.247, F.276, V.278, P.279 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:N.243, G:L.247 NAG-NAG-FUL.127: 6 residues within 4Å: Chain H: P.333, G.334, F.335, S.336, N.339, N.340 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.336, H:G.334 NAG-NAG-FUL.128: 8 residues within 4Å: Chain H: E.236, N.239, N.243, K.246, L.247, F.276, V.278, P.279 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:N.243, H:L.247

8 x GLY: GLYCINE(Non-covalent)

GLY.3: 5 residues within 4Å: Chain A: L.16, Y.59, W.96, D.127, K.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.96 Water bridges: A:K.129 Salt bridges: A:K.129 GLY.21: 5 residues within 4Å: Chain B: L.16, Y.59, W.96, D.127, K.129 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.96 Water bridges: B:K.129 Salt bridges: B:K.129 GLY.39: 5 residues within 4Å: Chain C: L.16, Y.59, W.96, D.127, K.129 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.96 Water bridges: C:K.129 Salt bridges: C:K.129 GLY.57: 5 residues within 4Å: Chain D: L.16, Y.59, W.96, D.127, K.129 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.96 Water bridges: D:K.129 Salt bridges: D:K.129 GLY.75: 5 residues within 4Å: Chain E: L.16, Y.59, W.96, D.127, K.129 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:W.96 Water bridges: E:K.129 Salt bridges: E:K.129 GLY.93: 5 residues within 4Å: Chain F: L.16, Y.59, W.96, D.127, K.129 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:W.96 Water bridges: F:K.129 Salt bridges: F:K.129 GLY.111: 5 residues within 4Å: Chain G: L.16, Y.59, W.96, D.127, K.129 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:W.96 Water bridges: G:K.129 Salt bridges: G:K.129 GLY.129: 5 residues within 4Å: Chain H: L.16, Y.59, W.96, D.127, K.129 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:W.96 Water bridges: H:K.129 Salt bridges: H:K.129

8 x VX: O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP(Covalent)

VX.4: 10 residues within 4Å: Chain A: G.113, G.114, G.115, S.196, A.197, W.229, L.284, V.286, H.436 Ligands: MG.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.286 Hydrogen bonds: A:G.114, A:G.115, A:A.197 VX.22: 10 residues within 4Å: Chain B: G.113, G.114, G.115, S.196, A.197, W.229, L.284, V.286, H.436 Ligands: MG.36 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.286 Hydrogen bonds: B:G.114, B:G.115, B:A.197 VX.40: 10 residues within 4Å: Chain C: G.113, G.114, G.115, S.196, A.197, W.229, L.284, V.286, H.436 Ligands: MG.54 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.286 Hydrogen bonds: C:G.114, C:G.115, C:A.197 VX.58: 10 residues within 4Å: Chain D: G.113, G.114, G.115, S.196, A.197, W.229, L.284, V.286, H.436 Ligands: MG.72 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.286 Hydrogen bonds: D:G.114, D:G.115, D:A.197 VX.76: 10 residues within 4Å: Chain E: G.113, G.114, G.115, S.196, A.197, W.229, L.284, V.286, H.436 Ligands: MG.90 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:V.286 Hydrogen bonds: E:G.114, E:G.115, E:A.197 VX.94: 10 residues within 4Å: Chain F: G.113, G.114, G.115, S.196, A.197, W.229, L.284, V.286, H.436 Ligands: MG.108 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:V.286 Hydrogen bonds: F:G.114, F:G.115, F:A.197 VX.112: 10 residues within 4Å: Chain G: G.113, G.114, G.115, S.196, A.197, W.229, L.284, V.286, H.436 Ligands: MG.126 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:V.286 Hydrogen bonds: G:G.114, G:G.115, G:A.197 VX.130: 10 residues within 4Å: Chain H: G.113, G.114, G.115, S.196, A.197, W.229, L.284, V.286, H.436 Ligands: MG.144 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:V.286 Hydrogen bonds: H:G.114, H:G.115, H:A.197

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

SO4.5: 4 residues within 4Å: Chain A: Q.314, G.411, N.412, N.413 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain A: R.518, F.519, F.523 Chain D: S.522, F.523 Ligands: SO4.60 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: Q.314, G.411, N.412, N.413 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain B: R.518, F.519, F.523 Chain C: S.522, F.523 Ligands: SO4.42 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain C: Q.314, G.411, N.412, N.413 Ligand excluded by PLIP SO4.42: 6 residues within 4Å: Chain B: S.522, F.523 Chain C: R.518, F.519, F.523 Ligands: SO4.24 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain D: Q.314, G.411, N.412, N.413 Ligand excluded by PLIP SO4.60: 6 residues within 4Å: Chain A: S.522, F.523 Chain D: R.518, F.519, F.523 Ligands: SO4.6 Ligand excluded by PLIP SO4.77: 4 residues within 4Å: Chain E: Q.314, G.411, N.412, N.413 Ligand excluded by PLIP SO4.78: 6 residues within 4Å: Chain E: R.518, F.519, F.523 Chain H: S.522, F.523 Ligands: SO4.132 Ligand excluded by PLIP SO4.95: 4 residues within 4Å: Chain F: Q.314, G.411, N.412, N.413 Ligand excluded by PLIP SO4.96: 6 residues within 4Å: Chain F: R.518, F.519, F.523 Chain G: S.522, F.523 Ligands: SO4.114 Ligand excluded by PLIP SO4.113: 4 residues within 4Å: Chain G: Q.314, G.411, N.412, N.413 Ligand excluded by PLIP SO4.114: 6 residues within 4Å: Chain F: S.522, F.523 Chain G: R.518, F.519, F.523 Ligands: SO4.96 Ligand excluded by PLIP SO4.131: 4 residues within 4Å: Chain H: Q.314, G.411, N.412, N.413 Ligand excluded by PLIP SO4.132: 6 residues within 4Å: Chain E: S.522, F.523 Chain H: R.518, F.519, F.523 Ligands: SO4.78 Ligand excluded by PLIP

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

NA.7: 3 residues within 4Å: Chain A: M.79, Y.438, E.441 Ligand excluded by PLIP NA.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.25: 3 residues within 4Å: Chain B: M.79, Y.438, E.441 Ligand excluded by PLIP NA.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.43: 3 residues within 4Å: Chain C: M.79, Y.438, E.441 Ligand excluded by PLIP NA.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.61: 3 residues within 4Å: Chain D: M.79, Y.438, E.441 Ligand excluded by PLIP NA.70: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.79: 3 residues within 4Å: Chain E: M.79, Y.438, E.441 Ligand excluded by PLIP NA.88: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.97: 3 residues within 4Å: Chain F: M.79, Y.438, E.441 Ligand excluded by PLIP NA.106: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.115: 3 residues within 4Å: Chain G: M.79, Y.438, E.441 Ligand excluded by PLIP NA.124: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.133: 3 residues within 4Å: Chain H: M.79, Y.438, E.441 Ligand excluded by PLIP NA.142: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

8 x K: POTASSIUM ION(Non-covalent)

K.8: 3 residues within 4Å: Chain A: F.523 Chain D: F.523 Ligands: K.62 No protein-ligand interaction detected (PLIP) K.26: 3 residues within 4Å: Chain B: F.523 Chain C: F.523 Ligands: K.44 No protein-ligand interaction detected (PLIP) K.44: 3 residues within 4Å: Chain B: F.523 Chain C: F.523 Ligands: K.26 No protein-ligand interaction detected (PLIP) K.62: 3 residues within 4Å: Chain A: F.523 Chain D: F.523 Ligands: K.8 No protein-ligand interaction detected (PLIP) K.80: 3 residues within 4Å: Chain E: F.523 Chain H: F.523 Ligands: K.134 No protein-ligand interaction detected (PLIP) K.98: 3 residues within 4Å: Chain F: F.523 Chain G: F.523 Ligands: K.116 No protein-ligand interaction detected (PLIP) K.116: 3 residues within 4Å: Chain F: F.523 Chain G: F.523 Ligands: K.98 No protein-ligand interaction detected (PLIP) K.134: 3 residues within 4Å: Chain E: F.523 Chain H: F.523 Ligands: K.80 No protein-ligand interaction detected (PLIP)

16 x CA: CALCIUM ION(Non-covalent)

CA.9: 1 residues within 4Å: Chain A: V.286 No protein-ligand interaction detected (PLIP) CA.17: 1 residues within 4Å: Chain A: N.83 No protein-ligand interaction detected (PLIP) CA.27: 1 residues within 4Å: Chain B: V.286 No protein-ligand interaction detected (PLIP) CA.35: 1 residues within 4Å: Chain B: N.83 No protein-ligand interaction detected (PLIP) CA.45: 1 residues within 4Å: Chain C: V.286 No protein-ligand interaction detected (PLIP) CA.53: 1 residues within 4Å: Chain C: N.83 No protein-ligand interaction detected (PLIP) CA.63: 1 residues within 4Å: Chain D: V.286 No protein-ligand interaction detected (PLIP) CA.71: 1 residues within 4Å: Chain D: N.83 No protein-ligand interaction detected (PLIP) CA.81: 1 residues within 4Å: Chain E: V.286 No protein-ligand interaction detected (PLIP) CA.89: 1 residues within 4Å: Chain E: N.83 No protein-ligand interaction detected (PLIP) CA.99: 1 residues within 4Å: Chain F: V.286 No protein-ligand interaction detected (PLIP) CA.107: 1 residues within 4Å: Chain F: N.83 No protein-ligand interaction detected (PLIP) CA.117: 1 residues within 4Å: Chain G: V.286 No protein-ligand interaction detected (PLIP) CA.125: 1 residues within 4Å: Chain G: N.83 No protein-ligand interaction detected (PLIP) CA.135: 1 residues within 4Å: Chain H: V.286 No protein-ligand interaction detected (PLIP) CA.143: 1 residues within 4Å: Chain H: N.83 No protein-ligand interaction detected (PLIP)

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

CL.10: 2 residues within 4Å: Chain A: R.345, Q.349 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: T.510 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain B: R.345, Q.349 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain B: T.510 Ligand excluded by PLIP CL.46: 2 residues within 4Å: Chain C: R.345, Q.349 Ligand excluded by PLIP CL.47: 1 residues within 4Å: Chain C: T.510 Ligand excluded by PLIP CL.64: 2 residues within 4Å: Chain D: R.345, Q.349 Ligand excluded by PLIP CL.65: 1 residues within 4Å: Chain D: T.510 Ligand excluded by PLIP CL.82: 2 residues within 4Å: Chain E: R.345, Q.349 Ligand excluded by PLIP CL.83: 1 residues within 4Å: Chain E: T.510 Ligand excluded by PLIP CL.100: 2 residues within 4Å: Chain F: R.345, Q.349 Ligand excluded by PLIP CL.101: 1 residues within 4Å: Chain F: T.510 Ligand excluded by PLIP CL.118: 2 residues within 4Å: Chain G: R.345, Q.349 Ligand excluded by PLIP CL.119: 1 residues within 4Å: Chain G: T.510 Ligand excluded by PLIP CL.136: 2 residues within 4Å: Chain H: R.345, Q.349 Ligand excluded by PLIP CL.137: 1 residues within 4Å: Chain H: T.510 Ligand excluded by PLIP

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

NAG.12: 3 residues within 4Å: Chain A: N.104, N.186, K.188 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: R.12, N.55 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: I.460, R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.254 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.104, N.186, K.188 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: R.12, N.55 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain B: I.460, R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.254 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.104, N.186, K.188 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: R.12, N.55 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain C: I.460, R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.254 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain D: N.104, N.186, K.188 Ligand excluded by PLIP NAG.67: 2 residues within 4Å: Chain D: R.12, N.55 Ligand excluded by PLIP NAG.68: 5 residues within 4Å: Chain D: I.460, R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.69: 1 residues within 4Å: Chain D: N.254 Ligand excluded by PLIP NAG.84: 3 residues within 4Å: Chain E: N.104, N.186, K.188 Ligand excluded by PLIP NAG.85: 2 residues within 4Å: Chain E: R.12, N.55 Ligand excluded by PLIP NAG.86: 5 residues within 4Å: Chain E: I.460, R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.87: 1 residues within 4Å: Chain E: N.254 Ligand excluded by PLIP NAG.102: 3 residues within 4Å: Chain F: N.104, N.186, K.188 Ligand excluded by PLIP NAG.103: 2 residues within 4Å: Chain F: R.12, N.55 Ligand excluded by PLIP NAG.104: 5 residues within 4Å: Chain F: I.460, R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.105: 1 residues within 4Å: Chain F: N.254 Ligand excluded by PLIP NAG.120: 3 residues within 4Å: Chain G: N.104, N.186, K.188 Ligand excluded by PLIP NAG.121: 2 residues within 4Å: Chain G: R.12, N.55 Ligand excluded by PLIP NAG.122: 5 residues within 4Å: Chain G: I.460, R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.123: 1 residues within 4Å: Chain G: N.254 Ligand excluded by PLIP NAG.138: 3 residues within 4Å: Chain H: N.104, N.186, K.188 Ligand excluded by PLIP NAG.139: 2 residues within 4Å: Chain H: R.12, N.55 Ligand excluded by PLIP NAG.140: 5 residues within 4Å: Chain H: I.460, R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.141: 1 residues within 4Å: Chain H: N.254 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-functional Binders)

MG.18: 1 residues within 4Å: Ligands: VX.4 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Ligands: VX.22 No protein-ligand interaction detected (PLIP) MG.54: 1 residues within 4Å: Ligands: VX.40 No protein-ligand interaction detected (PLIP) MG.72: 1 residues within 4Å: Ligands: VX.58 No protein-ligand interaction detected (PLIP) MG.90: 1 residues within 4Å: Ligands: VX.76 No protein-ligand interaction detected (PLIP) MG.108: 1 residues within 4Å: Ligands: VX.94 No protein-ligand interaction detected (PLIP) MG.126: 1 residues within 4Å: Ligands: VX.112 No protein-ligand interaction detected (PLIP) MG.144: 1 residues within 4Å: Ligands: VX.130 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wandhammer, M. et al., Structural Study of the Complex Stereoselectivity of Human Butyrylcholinesterase for the Neurotoxic V-Agents. J.Biol.Chem. (2011)

Release Date

2011-03-23

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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