SMTL ID : 1yaj.4 (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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.59 Water bridges: A:N.59 NAG.8: 2 residues within 4Å: Chain B: N.59 Chain C: D.240 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:D.240 Hydrogen bonds: B:N.59 Water bridges: B:V.57 NAG.14: 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, N.59, A.60, T.61, S.62 Chain B: K.242, T.257, T.258 Ligands: NAG.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.31, A:N.59, A:S.62, B:K.242 SIA.9: 12 residues within 4Å: Chain B: G.32, P.34, K.58, N.59, A.60, S.62, Y.63, P.64, P.65, Y.98 Chain C: K.242, T.257 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.32, B:N.59, B:Y.63 Salt bridges: B:K.58 SIA.15: 12 residues within 4Å: Chain A: K.242, T.257, T.258, S.259 Chain C: L.31, G.32, K.58, N.59, A.60, T.61, S.62, Y.98 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:K.242, A:S.259, C:N.59, C:T.61, C:S.62, C:S.62, C:Y.98 Salt bridges: A:K.242, C:K.58

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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.268, C:L.40 Salt bridges: A:H.264, A:R.267 SO4.4: 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 SO4.5: 5 residues within 4Å: Chain A: E.94, K.269, T.270, E.271 Chain B: H.264 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.44, A:E.94, A:E.271 Water bridges: A:E.272 Salt bridges: B:K.255, B:H.264 SO4.10: 3 residues within 4Å: Chain A: L.40 Chain B: H.264, R.267 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.264, B:R.267 SO4.11: 5 residues within 4Å: Chain B: R.44, E.94, T.270, E.271 Chain C: H.264 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Water bridges: C:K.255, B:R.44, B:R.44 Salt bridges: C:H.264, B:R.44 Hydrogen bonds: B:E.94, B:E.271 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(Covalent)(Non-covalent)

BEZ.6: 6 residues within 4Å: Chain A: G.122, G.123, S.201, A.202, I.339, H.447 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.339 Hydrogen bonds: A:G.123 BEZ.7: 3 residues within 4Å: Chain A: L.347, S.348, K.393 No protein-ligand interaction detected (PLIP) BEZ.12: 2 residues within 4Å: Chain B: S.201, L.284 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.284 Hydrogen bonds: B:S.201 Water bridges: B:G.123 BEZ.13: 3 residues within 4Å: Chain B: W.337, L.347, K.393 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.347, B:L.347 BEZ.17: 2 residues within 4Å: Chain C: S.201, V.234 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.234 Hydrogen bonds: C:S.201 BEZ.18: 2 residues within 4Å: Chain C: L.347, K.393 3 PLIP interactions: 3 interactions with chain C Water bridges: C:K.393, C:K.393 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
J

B
K

C
L

CES1 protein

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