SMTL ID : 1yaj.3 (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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.59 NAG.7: 1 residues within 4Å: Chain B: N.59 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain C: L.14, N.59 No protein-ligand interaction detected (PLIP)

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

SIA.2: 10 residues within 4Å: Chain A: L.31, G.32, K.58, N.59, T.61, S.62 Chain B: K.242, T.257, T.258 Ligands: NAG.1 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.32, A:N.59, A:S.62, A:S.62, B:K.242 Hydrophobic interactions: B:T.258 SIA.8: 7 residues within 4Å: Chain B: G.32, K.58, N.59, S.62, P.64 Chain C: K.242, T.257 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.59, B:N.59, B:N.59, B:S.62, C:K.242 Water bridges: B:T.61, B:S.62, C:S.259 Salt bridges: B:K.58 SIA.14: 8 residues within 4Å: Chain A: K.242, S.259 Chain C: L.31, G.32, N.59, A.60, S.62, Y.98 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:K.242, A:S.259, C:G.32, C:N.59, C:N.59, C:S.62 Salt bridges: A:K.242 Water bridges: C:S.62

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

SO4.3: 6 residues within 4Å: Chain A: H.264, R.267, Q.268 Chain C: L.40, G.41, P.42 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.268 Water bridges: A:R.267, A:R.267 Salt bridges: A:H.264, A:R.267 SO4.4: 7 residues within 4Å: Chain A: R.44, E.94, K.269, T.270, E.271 Chain B: K.255, H.264 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.94, A:E.271 Salt bridges: A:R.44, B:K.255, B:H.264 SO4.9: 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 SO4.10: 5 residues within 4Å: Chain B: R.44, E.94, T.270, E.271 Chain C: H.264 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Salt bridges: C:H.264, B:R.44 Hydrogen bonds: B:E.94, B:E.94, B:E.271 Water bridges: B:R.44 SO4.15: 5 residues within 4Å: Chain A: H.264 Chain C: R.44, E.94, T.270, E.271 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.44, C:E.94, C:E.271 Salt bridges: A:H.264 SO4.16: 2 residues within 4Å: Chain C: H.264, R.267 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Salt bridges: C:H.264, C:R.267 Water bridges: B:L.40

6 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.5: 4 residues within 4Å: Chain A: G.123, S.201, V.234, L.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.201 Water bridges: A:A.202 BEZ.6: 2 residues within 4Å: Chain A: L.347, K.393 No protein-ligand interaction detected (PLIP) BEZ.11: 3 residues within 4Å: Chain B: G.123, S.201, L.284 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.201, B:S.201 Water bridges: B:G.123 BEZ.12: 4 residues within 4Å: Chain B: W.337, L.347, S.348, K.393 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.393 Salt bridges: B:K.393 BEZ.17: 2 residues within 4Å: Chain C: S.201, L.342 No protein-ligand interaction detected (PLIP) BEZ.18: 2 residues within 4Å: Chain C: L.347, K.393 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.347 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
G

B
H

C
I

CES1 protein

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