SMTL ID : 2h7c.1 (3 other biounits)

Crystal structure of human carboxylesterase in complex with Coenzyme A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.61, T.63, S.64 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.18 NAG-NAG.2: 3 residues within 4Å: Chain F: L.16, N.61, T.63 No protein-ligand interaction detected (PLIP)

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

SO4.3: 2 residues within 4Å: Chain A: H.266, R.269 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:L.42 Water bridges: C:K.39, A:H.266 Salt bridges: A:H.266, A:R.269 SO4.4: 7 residues within 4Å: Chain A: R.46, E.96, K.271, T.272, E.273 Chain B: H.266, Q.270 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:Q.270, A:E.96, A:E.273 Salt bridges: B:H.266, A:R.46 Water bridges: A:R.46, A:R.46, A:E.274 SO4.7: 3 residues within 4Å: Chain A: P.44 Chain B: H.266, R.269 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.269, B:Q.270 Salt bridges: B:H.266, B:R.269 SO4.8: 5 residues within 4Å: Chain B: R.46, E.96, T.272, E.273 Chain C: H.266 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:E.273 Water bridges: B:R.46, B:R.46, B:R.46, B:E.96, B:E.274, C:H.266 Salt bridges: B:R.46, C:H.266 SO4.11: 6 residues within 4Å: Chain A: H.266, Q.270 Chain C: R.46, E.96, T.272, E.273 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.46, C:E.96, C:E.273, A:Q.270 Water bridges: C:K.271, C:E.274 Salt bridges: A:H.266 SO4.12: 5 residues within 4Å: Chain B: L.42, G.43 Chain C: H.266, R.269, Q.270 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.270 Water bridges: C:P.44, C:H.266, C:R.269 Salt bridges: C:H.266, C:R.269 SO4.16: 7 residues within 4Å: Chain D: H.266, Q.270 Chain E: R.46, E.96, K.271, T.272, E.273 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:E.273, D:Q.270 Water bridges: E:R.46, E:R.46, E:R.46, E:E.96, E:E.274 Salt bridges: E:R.46, D:H.266 SO4.17: 2 residues within 4Å: Chain D: H.266, R.269 3 PLIP interactions: 3 interactions with chain D Water bridges: D:H.266 Salt bridges: D:H.266, D:R.269 SO4.18: 5 residues within 4Å: Chain D: R.46, E.96, T.272, E.273 Chain F: H.266 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:R.46, D:E.96, D:E.273 Water bridges: D:E.274 Salt bridges: F:H.266 SO4.22: 5 residues within 4Å: Chain E: H.266, R.269, Q.270 Chain F: G.43, P.44 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Water bridges: F:L.42, E:H.266 Salt bridges: E:H.266, E:R.269 SO4.24: 6 residues within 4Å: Chain E: H.266 Chain F: R.46, E.96, K.271, T.272, E.273 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.46, F:E.96, F:E.273 Water bridges: F:G.43, F:K.271, F:E.273, F:E.273, F:E.274 Salt bridges: E:H.266 SO4.25: 6 residues within 4Å: Chain D: L.42, G.43, P.44 Chain F: H.266, R.269, Q.270 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:Q.270 Water bridges: F:A.262, F:H.266, F:R.269, F:R.269 Salt bridges: F:H.266, F:R.269

6 x COA: COENZYME A(Non-covalent)

COA.5: 22 residues within 4Å: Chain A: D.72, A.75, L.78, L.79, G.124, G.125, V.128, S.203, K.284, F.285, L.286, S.287, M.343, L.344, H.449 Chain F: L.281, K.284, S.287, L.288, L.290, S.346 Ligands: COA.26 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain F Hydrophobic interactions: A:L.286, A:L.344, A:L.344 Hydrogen bonds: A:D.72, A:D.72, A:D.72, A:S.203, A:S.287, A:S.287, F:L.281, F:S.287, F:S.287 Water bridges: A:D.72, A:G.125, A:G.125, A:F.285, F:S.346, F:S.346, F:S.346 COA.9: 25 residues within 4Å: Chain B: D.72, K.74, A.75, L.78, L.79, G.124, G.125, V.128, S.203, L.281, K.284, F.285, L.286, S.287, I.341, M.343, L.344, H.449 Chain D: L.281, K.282, K.284, S.287, L.288, L.290 Ligands: COA.19 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:L.286, B:L.344, B:L.344 Hydrogen bonds: B:D.72, B:D.72, B:S.203, B:S.287, B:S.287, D:K.282 Water bridges: B:D.72, B:G.124, B:G.125, B:K.284, B:F.285, D:L.288, D:L.290, D:L.290 pi-Cation interactions: D:K.284 COA.13: 26 residues within 4Å: Chain C: D.72, K.74, A.75, L.78, L.79, G.124, G.125, V.128, S.203, L.281, K.284, F.285, L.286, S.287, I.341, M.343, L.344, M.406, H.449 Chain E: L.281, K.284, S.287, L.288, L.290, S.346 Ligands: COA.23 21 PLIP interactions: 14 interactions with chain C, 7 interactions with chain E Hydrophobic interactions: C:L.286, C:L.344, C:L.344 Hydrogen bonds: C:D.72, C:D.72, C:D.72, C:S.203, C:S.287, C:S.287, E:K.282, E:K.284, E:S.287, E:S.346 Water bridges: C:D.72, C:G.125, C:G.125, C:F.285, C:F.285, E:K.284, E:K.284, E:S.346 COA.19: 23 residues within 4Å: Chain B: L.281, K.284, S.287, L.288, L.290, S.346 Chain D: D.72, K.74, A.75, L.79, G.124, G.125, V.128, S.203, K.284, F.285, L.286, S.287, M.343, L.344, F.407, H.449 Ligands: COA.9 19 PLIP interactions: 4 interactions with chain B, 15 interactions with chain D Hydrogen bonds: B:S.287, B:S.287, D:D.72, D:D.72, D:G.124, D:S.203, D:S.287, D:S.287 Water bridges: B:L.290, B:S.346, D:D.72, D:D.72, D:G.125, D:G.125, D:F.285, D:F.285 Hydrophobic interactions: D:L.286, D:L.344, D:L.344 COA.23: 23 residues within 4Å: Chain C: L.281, K.284, S.287, L.288, L.290, S.346 Chain E: D.72, K.74, A.75, L.78, L.79, G.124, G.125, V.128, S.203, K.284, F.285, L.286, S.287, M.343, L.344, H.449 Ligands: COA.13 19 PLIP interactions: 6 interactions with chain C, 13 interactions with chain E Hydrogen bonds: C:K.284, C:S.287, E:D.72, E:D.72, E:S.203, E:S.287, E:S.287 Water bridges: C:L.290, C:S.346, C:S.346, C:S.346, E:D.72, E:G.125, E:G.125, E:K.284, E:F.285 Hydrophobic interactions: E:L.286, E:L.344, E:L.344 COA.26: 25 residues within 4Å: Chain A: L.281, K.284, S.287, L.288, L.290, M.345, S.346 Chain F: D.72, A.75, L.79, G.124, G.125, V.128, S.203, K.284, F.285, L.286, S.287, I.341, M.343, L.344, M.406, F.407, H.449 Ligands: COA.5 17 PLIP interactions: 4 interactions with chain A, 13 interactions with chain F Hydrogen bonds: A:K.284, A:S.287, A:S.346, A:S.346, F:D.72, F:S.203, F:S.287 Hydrophobic interactions: F:L.286, F:L.344, F:L.344 Water bridges: F:D.72, F:D.72, F:G.124, F:G.125, F:F.285, F:F.285, F:S.346

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

NAG.6: 2 residues within 4Å: Chain B: N.61, T.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.61 NAG.10: 2 residues within 4Å: Chain C: N.61, T.63 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.61, C:T.63 NAG.14: 2 residues within 4Å: Chain D: N.61, T.63 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.61 Water bridges: D:T.63 NAG.20: 2 residues within 4Å: Chain E: N.61, T.63 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.63 Water bridges: E:N.61, E:T.63, E:T.63

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

SIA.15: 16 residues within 4Å: Chain D: L.33, G.34, P.36, K.60, N.61, S.64, Y.65, P.66, P.67, D.97, Y.100 Chain F: D.164, H.166, T.259, T.260, S.261 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:K.60, D:Y.100 Hydrogen bonds: D:G.34, D:S.64, D:S.64, D:S.64, D:S.64, D:Y.100, D:Y.100, F:S.261, F:S.261 Water bridges: D:T.63, F:A.262 SIA.21: 9 residues within 4Å: Chain D: K.244, T.260, S.261 Chain E: L.33, G.34, K.60, N.61, A.62, S.64 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:K.244, D:S.261, E:S.64, E:S.64, E:S.64 Water bridges: D:K.244, E:T.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bencharit, S. et al., Multisite promiscuity in the processing of endogenous substrates by human carboxylesterase 1. J.Mol.Biol. (2006)

Release Date

2006-08-29

Peptides

Liver carboxylesterase 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Liver carboxylesterase 1

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