SMTL ID : 2wg1.1

TERNARY COMPLEX OF THE AGED CONJUGATE OF TORPEDO CALIFORNICA ACEYLCHOLINESTERASE WITH SOMAN AND 2-PAM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NAG-FUC.1: 4 residues within 4Å: Chain A: N.59, S.61, T.62 Ligands: PEG.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.61

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

NAG.2: 3 residues within 4Å: Chain A: N.416, L.494 Ligands: PG4.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.494 Hydrogen bonds: A:N.416 Water bridges: A:N.416, A:N.416 NAG.21: 3 residues within 4Å: Chain B: N.416, L.494 Ligands: PG4.31 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.494 Hydrogen bonds: B:N.416 Water bridges: B:N.416, B:N.416

2 x GB: METHYLPHOSPHONIC ACID ESTER GROUP(Covalent)

GB.3: 10 residues within 4Å: Chain A: G.117, G.118, G.119, S.200, A.201, W.233, F.288, F.290, H.440 Ligands: FP1.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.118, A:G.119, A:A.201 GB.22: 10 residues within 4Å: Chain B: G.117, G.118, G.119, S.200, A.201, W.233, F.288, F.290, H.440 Ligands: FP1.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.118, B:G.119, B:A.201

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

FP1.4: 10 residues within 4Å: Chain A: W.84, G.117, G.118, E.199, F.330, I.439, H.440, G.441, Y.442 Ligands: GB.3 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:W.84 FP1.23: 10 residues within 4Å: Chain B: W.84, G.117, G.118, E.199, F.330, I.439, H.440, G.441, Y.442 Ligands: GB.22 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:W.84

8 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 5 residues within 4Å: Chain A: N.9, T.10, K.11, F.186 Ligands: PG4.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.9, A:N.9 MES.6: 10 residues within 4Å: Chain A: P.21, V.22, L.23, S.24, K.133, Y.134, L.452, V.453, K.454, E.455 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.23, A:Y.134 Salt bridges: A:K.133, A:E.455 MES.7: 9 residues within 4Å: Chain A: M.405, H.406, N.409, Q.500, R.515, V.518, C.521, V.522, N.525 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.409, A:Q.500, A:N.525 Water bridges: A:R.515 MES.8: 10 residues within 4Å: Chain A: S.79, G.80, M.83, N.429, L.430, V.431, W.432, Y.442, L.456, Y.458 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.431, A:W.432, A:Y.442 MES.24: 5 residues within 4Å: Chain B: N.9, T.10, K.11, F.186 Ligands: PG4.30 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.9, B:N.9 MES.25: 10 residues within 4Å: Chain B: P.21, V.22, L.23, S.24, K.133, Y.134, L.452, V.453, K.454, E.455 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.23 Salt bridges: B:K.133, B:E.455 MES.26: 9 residues within 4Å: Chain B: M.405, H.406, N.409, Q.500, R.515, V.518, C.521, V.522, N.525 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.409, B:Q.500, B:N.525 Water bridges: B:R.515 MES.27: 10 residues within 4Å: Chain B: S.79, G.80, M.83, N.429, L.430, V.431, W.432, Y.442, L.456, Y.458 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.431, B:W.432

8 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 6 residues within 4Å: Chain A: Y.70, Y.121, W.279, F.330, F.331, Y.334 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.121 Water bridges: A:Y.70, A:D.276, A:W.279 PG4.10: 11 residues within 4Å: Chain A: S.4, L.7, V.8, N.9, R.105, P.106, K.107, Q.185, F.186, G.188 Ligands: PG4.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.4, A:R.105, A:R.105, A:R.105, A:K.107 PG4.11: 5 residues within 4Å: Chain A: S.4, E.5, R.105 Ligands: MES.5, PG4.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.107 PG4.12: 4 residues within 4Å: Chain A: K.413, F.414, G.415 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.414 PG4.28: 6 residues within 4Å: Chain B: Y.70, Y.121, W.279, F.330, F.331, Y.334 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.70 Water bridges: B:Y.121, B:Y.121, B:D.276, B:W.279 PG4.29: 11 residues within 4Å: Chain B: S.4, L.7, V.8, N.9, R.105, P.106, K.107, Q.185, F.186, G.188 Ligands: PG4.30 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.4, B:S.4, B:R.105, B:R.105, B:R.105, B:K.107 PG4.30: 5 residues within 4Å: Chain B: S.4, E.5, R.105 Ligands: MES.24, PG4.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.107 PG4.31: 4 residues within 4Å: Chain B: K.413, F.414, G.415 Ligands: NAG.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.414

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.13: 6 residues within 4Å: Chain A: K.325, D.326, D.389, D.393, E.434, W.435 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.325, A:D.393 Water bridges: A:D.326, A:R.388, A:R.388, A:R.388, A:G.437 PGE.14: 4 residues within 4Å: Chain A: V.238, I.296, D.297, G.298 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.237, A:V.238, A:V.238, A:S.304, A:S.304 PGE.15: 6 residues within 4Å: Chain A: V.20, L.31, Y.63, W.100, N.131, K.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.131, A:N.131 Water bridges: A:K.133, A:K.133 PGE.32: 6 residues within 4Å: Chain B: K.325, D.326, D.389, D.393, E.434, W.435 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.325, B:D.393 Water bridges: B:R.388, B:R.388, B:R.388, B:E.434 PGE.33: 4 residues within 4Å: Chain B: V.238, I.296, D.297, G.298 5 PLIP interactions: 5 interactions with chain B Water bridges: B:S.237, B:V.238, B:V.238, B:S.304, B:S.304 PGE.34: 6 residues within 4Å: Chain B: V.20, L.31, Y.63, W.100, N.131, K.133 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.131, B:N.131 Water bridges: B:Y.63, B:K.133, B:K.133

10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.16: 7 residues within 4Å: Chain A: T.10, K.11, S.12, G.13, P.53, W.54, S.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.11 Water bridges: A:N.9 PEG.17: 5 residues within 4Å: Chain A: Q.374, Y.375, T.376, D.377 Chain B: Q.519 No protein-ligand interaction detected (PLIP) PEG.18: 3 residues within 4Å: Chain A: L.7, K.14, V.57 No protein-ligand interaction detected (PLIP) PEG.19: 5 residues within 4Å: Chain A: R.216, G.312, N.313, F.314, K.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.216, A:K.316 Water bridges: A:N.313, A:N.313 PEG.20: 6 residues within 4Å: Chain A: V.57, W.58, N.59, T.62 Ligands: NAG-FUC.1, NAG-FUC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.57, A:N.59 Water bridges: A:T.62 PEG.35: 7 residues within 4Å: Chain B: T.10, K.11, S.12, G.13, P.53, W.54, S.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.11 Water bridges: B:N.9 PEG.36: 5 residues within 4Å: Chain A: Q.519 Chain B: Q.374, Y.375, T.376, D.377 No protein-ligand interaction detected (PLIP) PEG.37: 3 residues within 4Å: Chain B: L.7, K.14, V.57 No protein-ligand interaction detected (PLIP) PEG.38: 5 residues within 4Å: Chain B: R.216, G.312, N.313, F.314, K.316 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.216, B:K.316 Water bridges: B:N.313, B:N.313 PEG.39: 4 residues within 4Å: Chain B: V.57, W.58, N.59, T.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.57, B:N.59 Water bridges: B:T.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanson, B. et al., Crystallographic Snapshots of Nonaged and Aged Conjugates of Soman with Acetylcholinesterase, and of a Ternary Complex of the Aged Conjugate with Pralidoxime. J.Med.Chem. (2009)

Release Date

2009-08-11

Peptides

ACETYLCHOLINESTERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ACETYLCHOLINESTERASE

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