SMTL ID : 7bwp.1

Crystal complex of endo-deglycosylated PcHNL5 with (R)-mandelonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x MXN: (2R)-hydroxy(phenyl)ethanenitrile(Non-covalent)

MXN.1: 11 residues within 4Å: Chain A: A.121, R.311, V.327, V.339, L.341, H.368, Y.468, W.469, H.470, H.508 Ligands: FAD.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.121, A:V.327, A:L.341, A:Y.468 pi-Stacking: A:W.469

6 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, L.141, N.145, D.186 Ligands: PEG.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.141 Hydrogen bonds: A:R.126, A:N.145, A:D.186 NAG.4: 8 residues within 4Å: Chain A: N.128, S.130, Q.134, H.187, A.189, I.332, S.334, Y.337 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.332 Hydrogen bonds: A:N.128, A:Q.134, A:Y.337 NAG.5: 7 residues within 4Å: Chain A: N.27, T.29, T.68, V.223, Q.224, S.249, D.250 7 PLIP interactions: 7 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 NAG.6: 3 residues within 4Å: Chain A: L.377, N.403, S.404 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.402, A:N.403 NAG.7: 3 residues within 4Å: Chain A: L.384, N.385, N.395 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.385, A:N.395

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

FAD.8: 31 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 Ligands: MXN.1 32 PLIP interactions: 32 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:G.511 pi-Cation interactions: A:H.470

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 7 residues within 4Å: Chain A: P.159, N.160, Q.162, F.198, D.199, N.200, V.326 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.160, A:S.196, A:S.196, A:N.200 Water bridges: A:N.200

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 4 residues within 4Å: Chain A: Y.132, L.141, N.145 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.141

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

Related Entries With Identical Sequence