SMTL ID : 2dqz.1

Crystal structure of human carboxylesterase in complex with homatropine, coenzyme A, and palmitate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.61 Chain B: D.242 Ligands: SIA.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.61 Hydrophobic interactions: B:D.242 NAG.8: 3 residues within 4Å: Chain B: L.16, N.61 Ligands: SIA.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.61 NAG.16: 3 residues within 4Å: Chain A: D.242 Chain C: N.61 Ligands: SIA.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.242

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

SIA.2: 7 residues within 4Å: Chain A: G.34, N.61, S.64, P.66 Chain B: K.244, T.259 Ligands: NAG.1 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.61, A:N.61, A:S.64, A:S.64, A:S.64, B:K.244, B:K.244 Water bridges: B:K.244 SIA.9: 6 residues within 4Å: Chain B: G.34, K.60, N.61, S.64 Chain C: K.244 Ligands: NAG.8 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:K.244, C:K.244, B:N.61, B:S.64, B:S.64 Water bridges: C:D.164, B:K.60, B:Y.100 Salt bridges: B:K.60 SIA.17: 7 residues within 4Å: Chain A: K.244, T.259 Chain C: G.34, K.60, N.61, Y.100 Ligands: NAG.16 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.61, C:N.61, A:K.244, A:K.244

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

SO4.3: 5 residues within 4Å: Chain A: H.266, R.269, Q.270 Chain C: L.42, G.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.270 Water bridges: A:R.269 Salt bridges: A:H.266, A:R.269 SO4.4: 6 residues within 4Å: Chain A: R.46, E.96, K.271, T.272, E.273 Chain B: H.266 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.273 Water bridges: A:G.43, A:R.46 Salt bridges: A:R.46, B:H.266 SO4.10: 5 residues within 4Å: Chain A: L.42, G.43, P.44 Chain B: H.266, R.269 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.270 Salt bridges: B:H.266, B:R.269 SO4.11: 5 residues within 4Å: Chain B: R.46, E.96, T.272, E.273 Chain C: H.266 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.273 Salt bridges: B:R.46, C:H.266 SO4.12: 2 residues within 4Å: Chain B: E.143, K.479 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.479 SO4.18: 6 residues within 4Å: Chain A: H.266 Chain C: R.46, E.96, K.271, T.272, E.273 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.271, C:E.273 Water bridges: C:R.46, C:R.46 Salt bridges: C:R.46, A:H.266 SO4.19: 2 residues within 4Å: Chain C: H.266, R.269 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.266, C:R.269

3 x F: FLUORIDE ION(Non-covalent)

F.5: 6 residues within 4Å: Chain A: G.123, G.124, G.125, S.203, A.204 Ligands: PLM.6 No protein-ligand interaction detected (PLIP) F.13: 6 residues within 4Å: Chain B: G.123, G.124, G.125, S.203, A.204 Ligands: PLM.14 No protein-ligand interaction detected (PLIP) F.20: 6 residues within 4Å: Chain C: G.123, G.124, G.125, S.203, A.204 Ligands: COA.21 No protein-ligand interaction detected (PLIP)

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.6: 7 residues within 4Å: Chain A: A.75, G.124, V.128, S.203, L.286, L.344 Ligands: F.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.75, A:V.128, A:L.286, A:L.344, A:L.344 PLM.14: 7 residues within 4Å: Chain B: A.75, G.124, V.128, S.203, L.286, L.344 Ligands: F.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.75, B:V.128, B:L.286, B:L.344, B:L.344 Hydrogen bonds: B:S.203 PLM.22: 12 residues within 4Å: Chain C: L.233, T.234, S.235, V.236, L.369, V.370, V.405, M.406, V.409, I.413, T.529, F.532 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.405, C:V.409, C:I.413, C:T.529, C:F.532 Hydrogen bonds: C:L.233, C:S.235, C:V.236

3 x HTQ: HOMOTROPINE(Non-covalent)

HTQ.7: 6 residues within 4Å: Chain A: W.339, M.343, Y.347, L.349, K.395, L.399 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.343, A:L.349 Salt bridges: A:K.395 HTQ.15: 8 residues within 4Å: Chain B: G.338, W.339, L.349, S.350, E.351, G.352, K.395, M.440 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.352 HTQ.23: 9 residues within 4Å: Chain C: G.338, W.339, L.349, S.350, K.395, D.396, L.399, P.442, V.445 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.339, C:K.395, C:L.399, C:P.442, C:V.445 Hydrogen bonds: C:L.349 Salt bridges: C:K.395

1 x COA: COENZYME A(Non-covalent)

COA.21: 4 residues within 4Å: Chain C: G.125, S.203, L.344 Ligands: F.20 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.344 Hydrogen bonds: C:S.203

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Liver carboxylesterase 1

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