SMTL ID : 1gxs.1

Crystal Structure of Hydroxynitrile Lyase from Sorghum bicolor in Complex with Inhibitor Benzoic Acid: a novel cyanogenic enzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- FUL- NAG: beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-FUL-NAG.1: 7 residues within 4Å: Chain A: G.36, R.37, A.38, Y.115, N.117 Chain B: S.30, I.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.30, B:S.30 NAG-FUL-NAG.2: 8 residues within 4Å: Chain C: G.36, R.37, A.38, Y.115, N.117 Chain D: V.29, S.30, I.32 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.29, D:I.32

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.3: 10 residues within 4Å: Chain A: G.62, G.63, P.64, D.126, S.158, H.160, F.161, W.270 Chain B: W.48, A.51 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.64, A:P.64, A:H.160, A:F.161, B:W.48, B:A.51 Hydrogen bonds: A:G.63 Water bridges: A:G.159 pi-Stacking: A:H.160 BEZ.6: 11 residues within 4Å: Chain C: G.62, G.63, P.64, D.126, S.158, H.160, F.161, M.228, W.270 Chain D: W.48, A.51 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.64, C:P.64, C:F.161, D:W.48, D:A.51 Hydrogen bonds: C:G.63 Water bridges: C:G.159, C:G.159 pi-Stacking: C:H.160

2 x DKA: DECANOIC ACID(Non-covalent)

DKA.4: 12 residues within 4Å: Chain A: N.61, G.62, G.63, L.71, E.157, N.249, Y.251, Y.265, F.269, W.270 Chain B: H.132, L.133 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.71, A:Y.251, A:Y.265, A:F.269 Hydrogen bonds: A:N.61, A:G.62, A:E.157 Salt bridges: B:H.132 DKA.7: 13 residues within 4Å: Chain C: N.61, G.62, G.63, C.66, L.71, E.157, N.249, Y.251, Y.265, F.269, W.270 Chain D: H.132, L.133 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.251, C:Y.265, C:F.269 Hydrogen bonds: C:N.61, C:G.62 Salt bridges: D:H.132

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

NAG.5: 10 residues within 4Å: Chain A: G.112, F.113 Chain B: N.17, Q.22, N.28, G.31, V.33, Y.35, P.36, W.37 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.33, A:F.113 Hydrogen bonds: B:Q.22, B:V.33, B:Y.35, B:W.37 NAG.8: 10 residues within 4Å: Chain C: G.112, F.113 Chain D: Q.22, N.28, G.31, V.33, E.34, Y.35, P.36, W.37 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.33 Hydrogen bonds: D:Q.22, D:N.28, D:V.33, D:Y.35, D:W.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lauble, H. et al., Crystal Structure of Hydroxynitrile Lyase from Sorghum Bicolor in Complex with the Inhibitor Benzoic Acid: A Novel Cyanogenic Enzyme. Biochemistry (2002)

Release Date

2002-10-01

Peptides

P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN A: AC
P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN A

P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN B