SMTL ID : 3gdp.2 (1 other biounit)

Hydroxynitrile lyase from almond, monoclinic crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-BMA-MAN-FUC.1: 2 residues within 4Å: Chain A: L.366, N.392 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN.2: 7 residues within 4Å: Chain A: R.116, T.119, D.132, N.135, H.171, D.176, E.178 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.170, A:H.171, A:E.178, A:D.176 Water bridges: A:H.171, A:S.174, A:S.174, A:D.176, A:E.178, A:E.178, A:E.178 Hydrophobic interactions: A:E.178

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 6 residues within 4Å: Chain A: I.121, S.125, F.490, Y.492, P.494, F.501 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.121, A:F.490, A:F.490, A:P.494, A:F.501 Hydrogen bonds: A:Y.492

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

FAD.4: 32 residues within 4Å: Chain A: G.33, G.35, T.36, S.37, L.54, E.55, R.56, V.98, G.100, R.101, V.102, G.105, T.106, S.107, N.110, A.111, G.112, V.113, A.215, V.217, S.256, A.257, G.258, V.379, W.458, H.459, D.486, G.487, H.497, P.498, Q.499, Y.502 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:T.106, A:N.110, A:W.458, A:W.458, A:W.458 Hydrogen bonds: A:T.36, A:T.36, A:S.37, A:R.56, A:R.56, A:G.100, A:V.102, A:T.106, A:N.110, A:A.111, A:V.113, A:V.113, A:V.217, A:V.217, A:G.487, A:Q.499, A:Q.499 Water bridges: A:G.35, A:G.38, A:R.99, A:T.106, A:T.106, A:T.259, A:T.259, A:W.458, A:H.459, A:G.500 pi-Cation interactions: A:H.459

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Post Translational Modification)

NDG.5: 3 residues within 4Å: Chain A: L.306, N.352, N.430 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.430, A:N.430 Water bridges: A:N.352

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

NAG.6: 9 residues within 4Å: Chain A: N.118, S.120, I.121, H.177, E.179, I.321, S.322, N.323, Y.326 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.321 Hydrogen bonds: A:N.118, A:N.323 Water bridges: A:N.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dreveny, I. et al., Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity. Biochemistry (2009)

Release Date

2009-03-24

Peptides

R-oxynitrile lyase isoenzyme 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

R-oxynitrile lyase isoenzyme 1

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