SMTL ID : 6jby.1

Crystal structure of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 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: 8 residues within 4Å: Chain A: N.128, S.130, Q.134, H.187, A.189, I.332, S.334, Y.337 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.334

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

NAG.2: 2 residues within 4Å: Chain A: S.290, N.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.292 Water bridges: A:S.290 NAG.3: 5 residues within 4Å: Chain A: R.126, I.129, L.141, N.145, D.186 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.141 Hydrogen bonds: A:R.126, A:N.145, A:D.186 Water bridges: A:L.141, A:N.145 NAG.4: 7 residues within 4Å: Chain A: N.27, T.29, T.68, V.223, Q.224, S.249, D.250 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.223 Hydrogen bonds: A:Q.224, A:Q.224, A:S.249 Water bridges: A:N.27, A:N.27 NAG.5: 2 residues within 4Å: Chain A: N.385, N.395 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.395 Water bridges: A:V.100, A:N.385 NAG.6: 2 residues within 4Å: Chain A: L.377, N.403 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.403 Water bridges: A:L.377, A:S.404, A:S.404, A:S.404, A:S.404

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

FAD.7: 30 residues within 4Å: Chain A: G.43, G.45, T.46, S.47, L.64, E.65, R.66, V.108, A.110, R.111, I.112, G.115, T.116, N.120, A.121, G.122, V.123, A.225, V.227, S.267, A.268, G.269, V.390, W.469, H.470, D.497, A.498, H.508, P.509, Q.510 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:T.116, A:N.120, A:W.469, A:W.469, A:W.469 Hydrogen bonds: A:G.44, A:T.46, A:T.46, A:S.47, A:R.66, A:R.66, A:A.110, A:I.112, A:T.116, A:N.120, A:A.121, A:V.123, A:V.123, A:V.227, A:V.227, A:A.498, A:Q.510 Water bridges: A:G.45, A:G.48, A:R.109, A:A.110, A:T.116, A:T.116, A:T.116, A:T.270, A:W.469, A:G.511 pi-Cation interactions: A:H.470

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

2020-04-01

Peptides

Hnl isoenzyme 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hnl isoenzyme 5

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