SMTL ID : 3rar.2 (1 other biounit)

X-ray structure of a bound phosphonate transition state analog and enantioselectivity of Candida rugosa lipase toward chiral carboxylic acids

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: Y.69, E.70, Y.299, S.300, N.351, Q.357 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.69, A:Y.69, A:E.70, A:Q.364 NAG-NAG.6: 6 residues within 4Å: Chain B: Y.69, E.70, Y.299, S.300, N.351, Q.357 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.69, B:Y.69, B:E.70, B:Q.364

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: W.221, N.222, V.313, N.314 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.221 Hydrogen bonds: A:N.222 NAG.7: 4 residues within 4Å: Chain B: W.221, N.222, V.313, N.314 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.221 Hydrogen bonds: B:N.222

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: D.260 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.260, A:D.260, H2O.6 CA.4: 4 residues within 4Å: Chain A: G.326 Chain B: G.326, Y.328 Ligands: CA.9 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:G.326, A:G.326, H2O.1 CA.8: 1 residues within 4Å: Chain B: D.260 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.260, B:D.260, H2O.13 CA.9: 4 residues within 4Å: Chain A: G.326, Y.328 Chain B: G.326 Ligands: CA.4 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:G.326, A:G.326, H2O.7

2 x IAN: methyl hydrogen (R)-[(R)-methoxy(phenyl)methyl]phosphonate(Covalent)

IAN.5: 13 residues within 4Å: Chain A: G.122, G.123, G.124, F.125, E.208, S.209, A.210, M.213, F.296, L.302, L.304, F.345, H.449 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.125, A:A.210, A:L.302, A:L.304, A:F.345 Hydrogen bonds: A:G.124, A:A.210 pi-Stacking: A:F.415 IAN.10: 13 residues within 4Å: Chain B: G.122, G.123, G.124, F.125, E.208, S.209, A.210, M.213, F.296, L.302, L.304, F.345, H.449 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.125, B:A.210, B:L.302, B:L.304, B:F.345 Hydrogen bonds: B:G.124, B:A.210 pi-Stacking: B:F.415

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Colton, I.J. et al., Insights into the molecular basis of chiral acid recognition by Candida rugosa lipase from an X-ray crystal structure of a bound phosphonate transition state analog. Adv.Synth.Catal. (2011)

Release Date

2011-04-27

Peptides

Lipase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lipase 1

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