SMTL ID : 1ya8.1

Crystal Structure of Human Liver Carboxylesterase in complex with cleavage products of Mevastatin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 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: N.59 Ligands: SIA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.59 Water bridges: A:N.59 NAG.7: 2 residues within 4Å: Chain B: N.59 Ligands: SIA.8 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: 8 residues within 4Å: Chain A: G.32, K.58, N.59, S.62, Y.98 Chain B: K.242, T.257 Ligands: NAG.1 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.59, A:N.59, A:N.59, A:T.61, A:S.62, A:S.62, A:S.62, B:K.242, B:K.242 SIA.8: 11 residues within 4Å: Chain B: L.31, G.32, K.58, N.59, S.62, P.64, Y.98 Chain C: K.242, T.258, S.259 Ligands: NAG.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:L.31, B:N.59, B:N.59, B:S.62, C:K.242 Water bridges: B:T.61, B:S.62, B:S.62 Salt bridges: B:K.58 SIA.14: 9 residues within 4Å: Chain A: K.242, T.258, S.259 Chain C: L.31, G.32, N.59, S.62, P.64, Y.98 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:K.242, A:K.242, A:S.259, C:L.31, C:N.59, C:N.59 Salt bridges: A:K.242 Water bridges: C:T.61, C:T.61, C:S.62, C:Y.98

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

SO4.3: 3 residues within 4Å: Chain A: H.264, R.267 Chain C: G.41 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 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Salt bridges: B:K.255, B:H.264, A:R.44 Hydrogen bonds: A:E.94, A:E.271 Water bridges: A:E.272 SO4.9: 5 residues within 4Å: Chain A: L.40, G.41 Chain B: H.264, R.267, Q.268 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.268 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 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.271 Water bridges: B:E.272 Salt bridges: B:R.44, C:H.264 SO4.15: 7 residues within 4Å: Chain A: H.264, Q.268 Chain C: R.44, E.94, K.269, T.270, E.271 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.268, C:R.44, C:E.271 Salt bridges: A:H.264 SO4.16: 4 residues within 4Å: Chain B: L.40 Chain C: H.264, R.267, Q.268 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.268 Salt bridges: C:H.264, C:R.267 Water bridges: B:L.40

2 x MVB: (1S,7S,8S,8AR)-1,2,3,7,8,8A-HEXAHYDRO-7-METHYL-8-[2-[(2R,4R)-TETRAHYDRO-4-HY DROXY-6-OXO-2H-PYRAN-2-YL]ETHYL]-1-NAPHTHALENOL(Non-covalent)

MVB.5: 8 residues within 4Å: Chain A: G.336, W.337, P.340, M.341, L.347, K.393, M.438, P.440 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.347 Salt bridges: A:K.393 MVB.17: 7 residues within 4Å: Chain C: G.336, L.347, S.348, K.393, L.397, M.438, P.440 6 PLIP interactions: 6 interactions with chain C Water bridges: C:W.337, C:Y.345, C:L.347, C:K.393, C:D.394 Salt bridges: C:K.393

4 x SMB: 2-METHYLBUTANOIC ACID(Non-covalent)

SMB.6: 3 residues within 4Å: Chain A: G.123, S.201, H.447 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.201, A:S.201 Water bridges: A:A.202 Salt bridges: A:H.447 SMB.11: 4 residues within 4Å: Chain B: G.122, G.123, S.201, H.447 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.201 Water bridges: B:G.122 Salt bridges: B:H.447 SMB.12: 2 residues within 4Å: Chain B: L.347, K.393 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.393 Salt bridges: B:K.393 SMB.18: 5 residues within 4Å: Chain C: G.122, G.123, S.201, L.284, H.447 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.284 Hydrogen bonds: C:G.123, C:S.201 Water bridges: C:G.122 Salt bridges: C:H.447

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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