SMTL ID : 4axb.1

Crystal structure of soman-aged human butyrylcholinesterase in complex with 2-PAM

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(Non-covalent)(Non-functional Binders)

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:G.334 NAG-NAG-FUL.2: 7 residues within 4Å: Chain A: Y.235, N.239, N.243, K.246, L.247, F.276, P.279 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.243, A:K.246, A:L.247 Hydrogen bonds: A:F.276 NAG-NAG-FUL.18: 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:G.334 NAG-NAG-FUL.19: 7 residues within 4Å: Chain B: Y.235, N.239, N.243, K.246, L.247, F.276, P.279 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.243, B:K.246, B:L.247 Hydrogen bonds: B:F.276 NAG-NAG-FUL.35: 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:G.334 NAG-NAG-FUL.36: 7 residues within 4Å: Chain C: Y.235, N.239, N.243, K.246, L.247, F.276, P.279 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.243, C:K.246, C:L.247 Hydrogen bonds: C:F.276 NAG-NAG-FUL.52: 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:G.334 NAG-NAG-FUL.53: 7 residues within 4Å: Chain D: Y.235, N.239, N.243, K.246, L.247, F.276, P.279 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.243, D:K.246, D:L.247 Hydrogen bonds: D:F.276 NAG-NAG-FUL.69: 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:G.334 NAG-NAG-FUL.70: 7 residues within 4Å: Chain E: Y.235, N.239, N.243, K.246, L.247, F.276, P.279 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:N.243, E:K.246, E:L.247 Hydrogen bonds: E:F.276 NAG-NAG-FUL.86: 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:G.334 NAG-NAG-FUL.87: 7 residues within 4Å: Chain F: Y.235, N.239, N.243, K.246, L.247, F.276, P.279 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:N.243, F:K.246, F:L.247 Hydrogen bonds: F:F.276 NAG-NAG-FUL.103: 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:G.334 NAG-NAG-FUL.104: 7 residues within 4Å: Chain G: Y.235, N.239, N.243, K.246, L.247, F.276, P.279 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:N.243, G:K.246, G:L.247 Hydrogen bonds: G:F.276 NAG-NAG-FUL.120: 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:G.334 NAG-NAG-FUL.121: 7 residues within 4Å: Chain H: Y.235, N.239, N.243, K.246, L.247, F.276, P.279 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:N.243, H:K.246, H:L.247 Hydrogen bonds: H:F.276

16 x K: POTASSIUM ION(Non-covalent)

K.3: 2 residues within 4Å: Chain A: Y.418, R.513 Ligand excluded by PLIP K.11: 3 residues within 4Å: Chain A: F.523 Chain D: F.523 Ligands: K.62 Ligand excluded by PLIP K.20: 2 residues within 4Å: Chain B: Y.418, R.513 Ligand excluded by PLIP K.28: 3 residues within 4Å: Chain B: F.523 Chain C: F.523 Ligands: K.45 Ligand excluded by PLIP K.37: 2 residues within 4Å: Chain C: Y.418, R.513 Ligand excluded by PLIP K.45: 3 residues within 4Å: Chain B: F.523 Chain C: F.523 Ligands: K.28 Ligand excluded by PLIP K.54: 2 residues within 4Å: Chain D: Y.418, R.513 Ligand excluded by PLIP K.62: 3 residues within 4Å: Chain A: F.523 Chain D: F.523 Ligands: K.11 Ligand excluded by PLIP K.71: 2 residues within 4Å: Chain E: Y.418, R.513 Ligand excluded by PLIP K.79: 3 residues within 4Å: Chain E: F.523 Chain H: F.523 Ligands: K.130 Ligand excluded by PLIP K.88: 2 residues within 4Å: Chain F: Y.418, R.513 Ligand excluded by PLIP K.96: 3 residues within 4Å: Chain F: F.523 Chain G: F.523 Ligands: K.113 Ligand excluded by PLIP K.105: 2 residues within 4Å: Chain G: Y.418, R.513 Ligand excluded by PLIP K.113: 3 residues within 4Å: Chain F: F.523 Chain G: F.523 Ligands: K.96 Ligand excluded by PLIP K.122: 2 residues within 4Å: Chain H: Y.418, R.513 Ligand excluded by PLIP K.130: 3 residues within 4Å: Chain E: F.523 Chain H: F.523 Ligands: K.79 Ligand excluded by PLIP

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

SO4.4: 4 residues within 4Å: Chain A: L.512, R.513, Q.516 Chain G: R.507 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain A: F.519, F.523 Chain D: S.522, F.523, K.526 Ligands: SO4.63 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: L.512, R.513, Q.516 Chain F: R.507 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain B: F.519, F.523 Chain C: S.522, F.523, K.526 Ligands: SO4.46 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain C: L.512, R.513, Q.516 Chain H: R.507 Ligand excluded by PLIP SO4.46: 6 residues within 4Å: Chain B: S.522, F.523, K.526 Chain C: F.519, F.523 Ligands: SO4.29 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain D: L.512, R.513, Q.516 Chain E: R.507 Ligand excluded by PLIP SO4.63: 6 residues within 4Å: Chain A: S.522, F.523, K.526 Chain D: F.519, F.523 Ligands: SO4.12 Ligand excluded by PLIP SO4.72: 4 residues within 4Å: Chain D: R.507 Chain E: L.512, R.513, Q.516 Ligand excluded by PLIP SO4.80: 6 residues within 4Å: Chain E: F.519, F.523 Chain H: S.522, F.523, K.526 Ligands: SO4.131 Ligand excluded by PLIP SO4.89: 4 residues within 4Å: Chain B: R.507 Chain F: L.512, R.513, Q.516 Ligand excluded by PLIP SO4.97: 6 residues within 4Å: Chain F: F.519, F.523 Chain G: S.522, F.523, K.526 Ligands: SO4.114 Ligand excluded by PLIP SO4.106: 4 residues within 4Å: Chain A: R.507 Chain G: L.512, R.513, Q.516 Ligand excluded by PLIP SO4.114: 6 residues within 4Å: Chain F: S.522, F.523, K.526 Chain G: F.519, F.523 Ligands: SO4.97 Ligand excluded by PLIP SO4.123: 4 residues within 4Å: Chain C: R.507 Chain H: L.512, R.513, Q.516 Ligand excluded by PLIP SO4.131: 6 residues within 4Å: Chain E: S.522, F.523, K.526 Chain H: F.519, F.523 Ligands: SO4.80 Ligand excluded by PLIP

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: K.43 Chain E: K.103 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: L.16, Y.59, W.96, D.127, K.129 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: W.229, T.232, E.236, R.240, L.284, S.285, V.286 Ligand excluded by PLIP GOL.22: 2 residues within 4Å: Chain B: K.43 Chain H: K.103 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: L.16, Y.59, W.96, D.127, K.129 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain B: W.229, T.232, E.236, R.240, L.284, S.285, V.286 Ligand excluded by PLIP GOL.39: 2 residues within 4Å: Chain C: K.43 Chain F: K.103 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain C: L.16, Y.59, W.96, D.127, K.129 Ligand excluded by PLIP GOL.47: 7 residues within 4Å: Chain C: W.229, T.232, E.236, R.240, L.284, S.285, V.286 Ligand excluded by PLIP GOL.56: 2 residues within 4Å: Chain D: K.43 Chain G: K.103 Ligand excluded by PLIP GOL.57: 5 residues within 4Å: Chain D: L.16, Y.59, W.96, D.127, K.129 Ligand excluded by PLIP GOL.64: 7 residues within 4Å: Chain D: W.229, T.232, E.236, R.240, L.284, S.285, V.286 Ligand excluded by PLIP GOL.73: 2 residues within 4Å: Chain C: K.103 Chain E: K.43 Ligand excluded by PLIP GOL.74: 5 residues within 4Å: Chain E: L.16, Y.59, W.96, D.127, K.129 Ligand excluded by PLIP GOL.81: 7 residues within 4Å: Chain E: W.229, T.232, E.236, R.240, L.284, S.285, V.286 Ligand excluded by PLIP GOL.90: 2 residues within 4Å: Chain A: K.103 Chain F: K.43 Ligand excluded by PLIP GOL.91: 5 residues within 4Å: Chain F: L.16, Y.59, W.96, D.127, K.129 Ligand excluded by PLIP GOL.98: 7 residues within 4Å: Chain F: W.229, T.232, E.236, R.240, L.284, S.285, V.286 Ligand excluded by PLIP GOL.107: 2 residues within 4Å: Chain B: K.103 Chain G: K.43 Ligand excluded by PLIP GOL.108: 5 residues within 4Å: Chain G: L.16, Y.59, W.96, D.127, K.129 Ligand excluded by PLIP GOL.115: 7 residues within 4Å: Chain G: W.229, T.232, E.236, R.240, L.284, S.285, V.286 Ligand excluded by PLIP GOL.124: 2 residues within 4Å: Chain D: K.103 Chain H: K.43 Ligand excluded by PLIP GOL.125: 5 residues within 4Å: Chain H: L.16, Y.59, W.96, D.127, K.129 Ligand excluded by PLIP GOL.132: 7 residues within 4Å: Chain H: W.229, T.232, E.236, R.240, L.284, S.285, V.286 Ligand excluded by PLIP

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

CL.7: 3 residues within 4Å: Chain A: Q.314, N.412, N.413 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: R.345 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: T.510 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain B: Q.314, N.412, N.413 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain B: R.345 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: T.510 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain C: Q.314, N.412, N.413 Ligand excluded by PLIP CL.43: 1 residues within 4Å: Chain C: R.345 Ligand excluded by PLIP CL.44: 1 residues within 4Å: Chain C: T.510 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain D: Q.314, N.412, N.413 Ligand excluded by PLIP CL.60: 1 residues within 4Å: Chain D: R.345 Ligand excluded by PLIP CL.61: 1 residues within 4Å: Chain D: T.510 Ligand excluded by PLIP CL.75: 3 residues within 4Å: Chain E: Q.314, N.412, N.413 Ligand excluded by PLIP CL.77: 1 residues within 4Å: Chain E: R.345 Ligand excluded by PLIP CL.78: 1 residues within 4Å: Chain E: T.510 Ligand excluded by PLIP CL.92: 3 residues within 4Å: Chain F: Q.314, N.412, N.413 Ligand excluded by PLIP CL.94: 1 residues within 4Å: Chain F: R.345 Ligand excluded by PLIP CL.95: 1 residues within 4Å: Chain F: T.510 Ligand excluded by PLIP CL.109: 3 residues within 4Å: Chain G: Q.314, N.412, N.413 Ligand excluded by PLIP CL.111: 1 residues within 4Å: Chain G: R.345 Ligand excluded by PLIP CL.112: 1 residues within 4Å: Chain G: T.510 Ligand excluded by PLIP CL.126: 3 residues within 4Å: Chain H: Q.314, N.412, N.413 Ligand excluded by PLIP CL.128: 1 residues within 4Å: Chain H: R.345 Ligand excluded by PLIP CL.129: 1 residues within 4Å: Chain H: T.510 Ligand excluded by PLIP

8 x FP1: N-hydroxy-1-(1-methylpyridin-2(1H)-ylidene)methanamine(Non-covalent)

FP1.8: 8 residues within 4Å: Chain A: W.80, G.113, G.114, E.195, X.196, A.326, H.436, Y.438 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.436 pi-Stacking: A:W.80 FP1.25: 8 residues within 4Å: Chain B: W.80, G.113, G.114, E.195, X.196, A.326, H.436, Y.438 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.436 pi-Stacking: B:W.80 FP1.42: 8 residues within 4Å: Chain C: W.80, G.113, G.114, E.195, X.196, A.326, H.436, Y.438 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.436 pi-Stacking: C:W.80 FP1.59: 8 residues within 4Å: Chain D: W.80, G.113, G.114, E.195, X.196, A.326, H.436, Y.438 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.436 pi-Stacking: D:W.80 FP1.76: 8 residues within 4Å: Chain E: W.80, G.113, G.114, E.195, X.196, A.326, H.436, Y.438 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.436 pi-Stacking: E:W.80 FP1.93: 8 residues within 4Å: Chain F: W.80, G.113, G.114, E.195, X.196, A.326, H.436, Y.438 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.436 pi-Stacking: F:W.80 FP1.110: 8 residues within 4Å: Chain G: W.80, G.113, G.114, E.195, X.196, A.326, H.436, Y.438 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:H.436 pi-Stacking: G:W.80 FP1.127: 8 residues within 4Å: Chain H: W.80, G.113, G.114, E.195, X.196, A.326, H.436, Y.438 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:H.436 pi-Stacking: H:W.80

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

NAG.14: 3 residues within 4Å: Chain A: N.104, N.186, K.188 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: R.12, N.55 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.254 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.104, N.186, K.188 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: R.12, N.55 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.34: 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: 4 residues within 4Å: Chain C: 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.65: 3 residues within 4Å: Chain D: N.104, N.186, K.188 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain D: R.12, N.55 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain D: R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.68: 1 residues within 4Å: Chain D: N.254 Ligand excluded by PLIP NAG.82: 3 residues within 4Å: Chain E: N.104, N.186, K.188 Ligand excluded by PLIP NAG.83: 2 residues within 4Å: Chain E: R.12, N.55 Ligand excluded by PLIP NAG.84: 4 residues within 4Å: Chain E: R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.85: 1 residues within 4Å: Chain E: N.254 Ligand excluded by PLIP NAG.99: 3 residues within 4Å: Chain F: N.104, N.186, K.188 Ligand excluded by PLIP NAG.100: 2 residues within 4Å: Chain F: R.12, N.55 Ligand excluded by PLIP NAG.101: 4 residues within 4Å: Chain F: R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.102: 1 residues within 4Å: Chain F: N.254 Ligand excluded by PLIP NAG.116: 3 residues within 4Å: Chain G: N.104, N.186, K.188 Ligand excluded by PLIP NAG.117: 2 residues within 4Å: Chain G: R.12, N.55 Ligand excluded by PLIP NAG.118: 4 residues within 4Å: Chain G: R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.119: 1 residues within 4Å: Chain G: N.254 Ligand excluded by PLIP NAG.133: 3 residues within 4Å: Chain H: N.104, N.186, K.188 Ligand excluded by PLIP NAG.134: 2 residues within 4Å: Chain H: R.12, N.55 Ligand excluded by PLIP NAG.135: 4 residues within 4Å: Chain H: R.463, K.467, E.480, N.483 Ligand excluded by PLIP NAG.136: 1 residues within 4Å: Chain H: N.254 Ligand excluded by PLIP

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