SMTL ID : 2hrr.1

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

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: 10 residues within 4Å: Chain A: G.336, W.337, P.340, M.341, L.347, S.348, G.350, K.393, L.397, M.438 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.438, A:G.336, A:L.347, A:K.393, A:K.393 GLC-FRU.2: 9 residues within 4Å: Chain B: G.336, W.337, P.340, M.341, L.347, S.348, G.350, K.393, L.397 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.393, B:G.336, B:D.394 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 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.336, C:K.393, C:K.393 Water bridges: C:P.340, C:M.341, C:L.347

3 x NTJ: R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE(Covalent)

NTJ.4: 9 residues within 4Å: Chain A: F.81, G.121, G.122, G.123, E.200, S.201, A.202, V.234, H.447 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.234 Hydrogen bonds: A:G.122, A:G.123, A:A.202 Salt bridges: A:E.200 NTJ.9: 10 residues within 4Å: Chain B: L.77, F.81, G.121, G.122, G.123, S.201, A.202, V.234, I.339, H.447 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.234 Hydrogen bonds: B:G.122, B:G.123, B:A.202 NTJ.13: 9 residues within 4Å: Chain C: F.81, G.121, G.122, G.123, E.200, S.201, A.202, V.234, H.447 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.234 Hydrogen bonds: C:G.122, C:G.123, C:A.202 Salt bridges: C:E.200

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

NAG.5: 2 residues within 4Å: Chain A: N.59, T.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.61, A:T.61 NAG.10: 3 residues within 4Å: Chain B: N.59 Chain C: D.240 Ligands: SIA.11 No protein-ligand interaction detected (PLIP) NAG.15: 4 residues within 4Å: Chain A: D.240 Chain C: L.14, N.59 Ligands: SIA.16 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.240 Water bridges: A:D.240 Hydrophobic interactions: C:L.14

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

SIA.6: 10 residues within 4Å: Chain A: L.31, G.32, K.58, N.59, S.62, Y.63, P.64, P.65 Chain B: K.242, T.257 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.59, A:N.59, A:S.62, A:S.62 Water bridges: A:S.62 Salt bridges: B:K.242 SIA.11: 9 residues within 4Å: Chain B: G.32, K.58, N.59, S.62, Y.63, P.64, Y.98 Chain C: K.242 Ligands: NAG.10 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:N.59 Hydrogen bonds: B:N.59, B:N.59, B:N.59, B:S.62, B:S.62, C:K.242 Water bridges: B:K.58, B:T.61, B:T.61, B:S.62 Salt bridges: B:K.58 SIA.16: 8 residues within 4Å: Chain C: L.31, G.32, K.58, N.59, A.60, S.62, Y.98 Ligands: NAG.15 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:K.242, A:K.242, C:G.32, C:N.59, C:T.61, C:S.62, C:S.62 Water bridges: A:D.162, A:D.162, A:D.162, A:K.242 Salt bridges: C:K.58

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

SO4.7: 3 residues within 4Å: Chain A: V.263, H.264, R.267 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.264, A:R.267 SO4.8: 6 residues within 4Å: Chain A: R.44, E.94, K.269, T.270, E.271 Chain B: H.264 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.264, A:R.44, A:E.271 SO4.12: 4 residues within 4Å: Chain A: L.40 Chain B: A.260, H.264, R.267 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:P.38, B:R.267, B:R.267 Salt bridges: B:H.264, B:R.267 SO4.14: 7 residues within 4Å: Chain A: H.264, Q.268 Chain C: R.44, E.94, K.269, T.270, E.271 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Salt bridges: A:H.264 Hydrogen bonds: C:R.44, C:K.269, C:E.271 Water bridges: C:E.94 SO4.17: 3 residues within 4Å: Chain B: L.40 Chain C: H.264, R.267 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain C Water bridges: B:L.40, C:H.264, C:H.264, C:H.264, C:H.264, C:R.267, C:Q.268 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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