SMTL ID : 6lqy.1

Crystal complex of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis with benzaldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: N.23, T.25, T.64, V.219, Q.220, S.245, D.246 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.219, A:Q.220 Hydrogen bonds: A:Q.220, A:Q.220, A:S.245 Water bridges: A:N.23, A:N.23, A:Q.220, A:Q.220 NAG.2: 2 residues within 4Å: Chain A: S.286, N.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.288 Water bridges: A:S.286 NAG.3: 4 residues within 4Å: Chain A: R.122, L.137, N.141, D.182 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.137 Hydrogen bonds: A:R.122, A:N.141, A:D.182 NAG.4: 3 residues within 4Å: Chain A: L.380, N.381, N.391 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.391 NAG.5: 2 residues within 4Å: Chain A: L.373, N.399 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.399 NAG.6: 8 residues within 4Å: Chain A: N.124, S.126, Q.130, H.183, A.185, I.328, S.330, Y.333 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.328 Hydrogen bonds: A:N.124, A:Q.130, A:S.330, A:Y.333 Water bridges: A:S.330, A:S.330 NAG.7: 5 residues within 4Å: Chain A: H.6, L.7, A.8, N.9, D.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.7, A:N.9

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.8: 30 residues within 4Å: Chain A: G.39, G.41, T.42, S.43, L.60, E.61, R.62, V.104, A.106, R.107, I.108, G.111, T.112, N.116, A.117, G.118, V.119, A.221, V.223, S.263, A.264, G.265, V.386, W.465, H.466, D.493, A.494, H.504, P.505, Q.506 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:V.104, A:T.112, A:N.116, A:W.465, A:W.465, A:W.465 Hydrogen bonds: A:G.40, A:T.42, A:T.42, A:S.43, A:R.62, A:R.62, A:A.106, A:I.108, A:T.112, A:N.116, A:A.117, A:V.119, A:V.119, A:V.223, A:V.223, A:A.494, A:Q.506 Water bridges: A:G.41, A:R.105, A:A.106, A:T.112, A:T.112, A:T.112, A:T.266, A:G.507

1 x HBX: benzaldehyde(Non-covalent)

HBX.9: 8 residues within 4Å: Chain A: A.117, R.307, V.335, L.337, H.364, Y.464, W.465, H.504 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.117, A:L.337 pi-Stacking: A:W.465

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, Y.C. et al., Structure-Guided Tuning of a Hydroxynitrile Lyase to Accept Rigid Pharmaco Aldehydes. Acs Catalysis (2020)

Release Date

2020-05-13

Peptides

PREDICTED: (R)-mandelonitrile lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PREDICTED: (R)-mandelonitrile lyase