SMTL ID : 7cgs.1

Crystal endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L343F from Prunus communis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

FAD.1: 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 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:V.108, 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:A.110, A:T.116, A:T.116, A:T.270, A:W.469, A:G.511 pi-Cation interactions: A:H.470

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

NAG.2: 2 residues within 4Å: Chain A: L.377, N.403 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.403 Water bridges: A:N.403, A:T.405 NAG.3: 2 residues within 4Å: Chain A: N.385, N.395 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.395 Water bridges: A:V.100 NAG.4: 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.5: 2 residues within 4Å: Chain A: T.14, N.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.201 Water bridges: A:N.201, A:N.201 NAG.6: 5 residues within 4Å: Chain A: R.126, L.141, D.142, N.145, D.186 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.141 Hydrogen bonds: A:R.126, A:D.142, A:N.145, A:D.186 Water bridges: A:L.141, A:N.145 NAG.7: 8 residues within 4Å: Chain A: N.128, S.130, Q.134, H.187, A.189, I.332, S.334, Y.337 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.332 Hydrogen bonds: A:N.128, A:Q.134, A:S.334, A:Y.337 Water bridges: A:N.128 NAG.8: 7 residues within 4Å: Chain A: N.27, T.29, T.68, V.223, Q.224, S.249, D.250 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.223, A:Q.224 Hydrogen bonds: A:Q.224, A:Q.224, A:S.249 Water bridges: A:N.27, A:N.27, A:N.27 NAG.9: 5 residues within 4Å: Chain A: H.10, L.11, A.12, N.13, D.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.11, A:N.13 Water bridges: A:N.13

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.10: 3 residues within 4Å: Chain A: Y.26, D.30, S.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.30, A:S.32, A:S.32

1 x BCN: BICINE(Non-covalent)

BCN.11: 5 residues within 4Å: Chain A: S.166, G.169, E.170, D.180, G.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.170, A:G.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, Y.C. et al., A High-Throughput Screening Method for the Directed Evolution of Hydroxynitrile Lyase towards Cyanohydrin Synthesis. Chembiochem (2021)

Release Date

2021-04-21

Peptides

(R)-mandelonitrile lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

(R)-mandelonitrile lyase