SMTL ID : 1yaj.1 (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: 2 residues within 4Å: Chain A: P.3, N.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.59 NAG.8: 3 residues within 4Å: Chain B: L.14, N.59 Ligands: SIA.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.59 NAG.14: 2 residues within 4Å: Chain A: D.240 Chain C: N.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.240

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

SIA.2: 9 residues within 4Å: Chain A: L.31, G.32, N.59, A.60, S.62, Y.98 Chain B: K.242, T.257, T.258 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.258 Hydrogen bonds: B:K.242, B:K.242, A:L.31, A:N.59, A:S.62, A:S.62 Water bridges: B:S.259 Salt bridges: B:K.242 SIA.3: 9 residues within 4Å: Chain A: D.162, K.242, T.258, S.259 Chain C: L.31, G.32, K.58, N.59, Y.98 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.32, C:N.59, C:N.59, A:K.242, A:S.259 Salt bridges: C:K.58, A:K.242 SIA.9: 9 residues within 4Å: Chain B: L.31, G.32, K.58, N.59, A.60, S.62, P.64 Chain C: K.242 Ligands: NAG.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.31, B:N.59, B:N.59, B:S.62 Salt bridges: B:K.58

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

SO4.4: 5 residues within 4Å: Chain A: H.264, R.267 Chain C: L.40, G.41, P.42 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.264, A:R.267 SO4.5: 7 residues within 4Å: Chain A: R.44, E.94, K.269, T.270, E.271 Chain B: H.264, Q.268 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.271 Salt bridges: A:R.44, B:H.264 SO4.10: 5 residues within 4Å: Chain A: L.40, 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 SO4.11: 7 residues within 4Å: Chain B: R.44, E.94, K.269, T.270, E.271 Chain C: K.255, H.264 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.269, B:E.271 Salt bridges: B:R.44, C:K.255, C:H.264 SO4.15: 6 residues within 4Å: Chain A: H.264 Chain C: R.44, E.94, K.269, T.270, E.271 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.94, C:E.271 Water bridges: C:E.272 Salt bridges: C:R.44, A:H.264 SO4.16: 4 residues within 4Å: Chain B: L.40 Chain C: H.264, R.267, Q.268 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.268 Salt bridges: C:H.264, C:R.267

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

BEZ.6: 4 residues within 4Å: Chain A: L.77, S.201, L.284, L.342 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.77, A:L.284, A:L.342 Water bridges: A:G.123 BEZ.7: 4 residues within 4Å: Chain A: W.337, L.347, S.348, K.393 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.393 Salt bridges: A:K.393 BEZ.12: 1 residues within 4Å: Chain B: L.347 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.347 Salt bridges: B:K.393 BEZ.13: 4 residues within 4Å: Chain B: G.123, S.201, V.234, L.284 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.234, B:L.284 Hydrogen bonds: B:S.201, B:S.201 Water bridges: B:G.122 BEZ.17: 8 residues within 4Å: Chain C: G.121, G.122, G.123, S.201, A.202, L.284, I.339, H.447 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.284, C:I.339, C:I.339 Hydrogen bonds: C:G.122, C:G.123, C:A.202 BEZ.18: 3 residues within 4Å: Chain C: L.347, S.348, K.393 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.393

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
A

B
B

C
C

CES1 protein

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