SMTL ID : 2hrq.1 (1 other biounit)

Crystal structure of Human Liver Carboxylesterase 1 (hCE1) in covalent complex with the nerve agent Soman (GD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

3 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 9 residues within 4Å: Chain A: G.336, W.337, M.341, L.347, S.348, G.350, K.393, L.397, M.438 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.348, A:M.438, A:G.336, A:K.393, A:K.393 GLC-FRU.2: 7 residues within 4Å: Chain B: G.336, W.337, L.347, S.348, G.350, K.393, L.397 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.336, B:K.393, B:K.393 GLC-FRU.3: 8 residues within 4Å: Chain C: G.336, W.337, M.341, L.347, S.348, G.350, K.393, L.397 5 PLIP interactions: 5 interactions with chain C Water bridges: C:K.393, C:P.340, C:L.347 Hydrogen bonds: C:G.336, C:K.393, C:K.393

3 x GD7: (1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE(Covalent)

GD7.4: 11 residues within 4Å: Chain A: G.121, G.122, G.123, S.201, A.202, L.235, L.284, L.298, L.367, M.404, H.447 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.235, A:L.284, A:L.298, A:L.367 Hydrogen bonds: A:G.122, A:G.123, A:A.202 GD7.9: 11 residues within 4Å: Chain B: G.121, G.122, G.123, S.201, A.202, L.284, L.298, I.339, M.404, F.405, H.447 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.284, B:L.298, B:I.339, B:F.405 Hydrogen bonds: B:G.122, B:G.123, B:A.202 GD7.14: 12 residues within 4Å: Chain C: G.121, G.122, G.123, S.201, A.202, V.234, L.284, L.298, I.339, M.404, F.405, H.447 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.234, C:L.284, C:L.298, C:I.339, C:F.405 Hydrogen bonds: C:G.122, C:G.123, C:A.202

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

NAG.5: 1 residues within 4Å: Chain A: N.59 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.61 NAG.10: 3 residues within 4Å: Chain B: N.59 Chain C: D.240 Ligands: SIA.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.59 NAG.16: 3 residues within 4Å: Chain A: D.240 Chain C: N.59 Ligands: SIA.17 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:N.59 Hydrogen bonds: A:D.240

3 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.6: 7 residues within 4Å: Chain A: L.31, G.32, K.58, N.59, S.62, Y.98 Chain B: K.242 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:N.59 Hydrogen bonds: A:K.58, A:N.59, A:N.59, A:S.62, A:S.62, A:S.62, A:S.62, B:K.242 Water bridges: A:K.58, A:Y.98 Salt bridges: B:K.242 SIA.11: 8 residues within 4Å: Chain B: G.32, K.58, N.59, S.62, Y.63, P.64 Chain C: K.242 Ligands: NAG.10 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:N.59 Hydrogen bonds: B:N.59, B:N.59, B:S.62, B:Y.63 Water bridges: B:K.58, B:T.61, B:T.61, B:Y.98, B:Y.98, C:K.242, C:K.242 Salt bridges: B:K.58 SIA.17: 6 residues within 4Å: Chain A: K.242 Chain C: L.31, G.32, N.59, S.62 Ligands: NAG.16 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain C Salt bridges: A:K.242 Hydrogen bonds: C:N.59, C:N.59, C:N.59, C:S.62, C:S.62 Water bridges: C:T.61, C:T.61

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

SO4.7: 3 residues within 4Å: Chain A: H.264, R.267 Chain C: L.40 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Salt bridges: A:H.264, A:R.267 Hydrogen bonds: C:L.40 SO4.8: 6 residues within 4Å: Chain A: R.44, E.94, T.270, E.271 Chain B: H.264, Q.268 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.44, A:E.94, A:E.271 Water bridges: A:E.272, B:Q.268, B:Q.268 Salt bridges: B:H.264 SO4.12: 4 residues within 4Å: Chain A: L.40, P.42 Chain B: H.264, R.267 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.264, B:R.267 SO4.13: 7 residues within 4Å: Chain B: R.44, E.94, T.270, E.271, E.272 Chain C: H.264, Q.268 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.44, B:K.269, B:E.271 Salt bridges: C:H.264 SO4.15: 8 residues within 4Å: Chain A: H.264, Q.268 Chain C: R.44, E.94, K.269, T.270, E.271, E.272 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Water bridges: A:Q.268, A:Q.268 Salt bridges: A:H.264 Hydrogen bonds: C:R.44, C:E.94, C:E.271 SO4.18: 3 residues within 4Å: Chain B: P.42 Chain C: H.264, R.267 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.264, C:R.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fleming, C.D. et al., Crystal Structures of Human Carboxylesterase 1 in Covalent Complexes with the Chemical Warfare Agents Soman and Tabun. Biochemistry (2007)

Release Date

2007-05-01

Peptides

Liver carboxylesterase 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Liver carboxylesterase 1

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