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

Crystal Structure of Human Liver Carboxylesterase in complex with benzil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 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.59 Chain B: D.240 Ligands: SIA.2 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: N.59 Ligands: SIA.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.57 NAG.13: 4 residues within 4Å: Chain A: D.240, K.242 Chain C: N.59 Ligands: SIA.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.242, A:K.242, C:N.59

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

SIA.2: 10 residues within 4Å: Chain A: G.32, K.58, N.59, A.60, T.61, S.62 Chain B: K.242, T.257, T.258 Ligands: NAG.1 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.59, A:T.61, A:S.62, A:S.62, B:K.242, B:K.242 Hydrophobic interactions: B:T.258 Water bridges: B:S.259 SIA.8: 11 residues within 4Å: Chain B: L.31, G.32, K.58, N.59, S.62, Y.63, P.64, P.65 Chain C: K.242, T.257 Ligands: NAG.7 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.59, B:N.59, B:S.62, B:S.62, B:Y.98, C:K.242, C:K.242 Salt bridges: B:K.58, C:K.242 SIA.14: 10 residues within 4Å: Chain A: D.162, K.242, T.258, S.259 Chain C: G.32, P.34, K.58, N.59, S.62 Ligands: NAG.13 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:S.259, C:K.58, C:S.62 Salt bridges: A:K.242 Water bridges: C:L.31, C:S.62

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

SO4.3: 4 residues within 4Å: Chain A: H.264, R.267 Chain C: L.40, P.42 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.264, A:R.267 SO4.4: 6 residues within 4Å: Chain A: R.44, E.94, K.269, T.270, E.271 Chain B: H.264 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.269, A:E.271 Salt bridges: A:R.44, B:H.264 SO4.9: 4 residues within 4Å: Chain A: G.41, P.42 Chain B: H.264, R.267 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.264, B:R.267 SO4.10: 6 residues within 4Å: Chain B: R.44, E.94, K.269, T.270, E.271 Chain C: H.264 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.94, B:E.271 Salt bridges: B:R.44, C:H.264 SO4.15: 7 residues within 4Å: Chain A: H.264 Chain C: G.41, R.44, E.94, K.269, T.270, E.271 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.41, C:E.271 Salt bridges: C:R.44, A:H.264 SO4.16: 3 residues within 4Å: Chain B: G.41 Chain C: H.264, R.267 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.264 Salt bridges: C:H.264, C:R.267

6 x BEZ: BENZOIC ACID(Non-covalent)(Covalent)

BEZ.5: 5 residues within 4Å: Chain A: L.77, S.201, L.284, L.298, L.342 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.77, A:L.284, A:L.342 Hydrogen bonds: A:S.201 Water bridges: A:A.202 BEZ.6: 3 residues within 4Å: Chain A: L.347, S.348, K.393 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.393, A:K.393 Salt bridges: A:K.393 BEZ.11: 2 residues within 4Å: Chain B: P.340, K.393 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.340 BEZ.12: 2 residues within 4Å: Chain B: S.201, L.342 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.342 Water bridges: B:A.202 BEZ.17: 8 residues within 4Å: Chain C: L.77, G.122, G.123, S.201, A.202, L.284, I.339, H.447 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.77, C:L.284, C:I.339, C:I.339 Hydrogen bonds: C:A.202 BEZ.18: 2 residues within 4Å: Chain C: L.347, K.393 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fleming, C.D. et al., Structural insights into drug processing by human carboxylesterase 1: tamoxifen, mevastatin, and inhibition by benzil. J.Mol.Biol. (2005)

Release Date

2005-08-02

Peptides

CES1 protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

CES1 protein

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