SMTL ID : 5yot.1

Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

7 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: 4 residues within 4Å: Chain A: N.51, G.54, W.57 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.57 NAG-NAG.2: 4 residues within 4Å: Chain A: W.458, R.487, N.497 Chain B: L.615 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: S.190, N.192, M.353, G.354 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.51, G.54 Ligands: NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: S.190, N.192, M.353, G.354 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: L.615 Chain B: W.458, R.487, N.497 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.458 NAG-NAG.7: 4 residues within 4Å: Chain B: P.542, S.545, N.546, W.629 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 2 residues within 4Å: Chain A: D.684, V.686 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.684, A:V.686, H2O.2, H2O.2, H2O.3, H2O.3 CA.19: 2 residues within 4Å: Chain B: D.684, V.686 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.684, B:V.686, H2O.19, H2O.21, H2O.23, H2O.26

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

NAG.9: 3 residues within 4Å: Chain A: N.44, T.47 Ligands: NAG-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.44 NAG.10: 3 residues within 4Å: Chain A: L.52, Q.90, N.91 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.52 Water bridges: A:N.91, A:N.91 NAG.11: 4 residues within 4Å: Chain A: P.542, S.545, N.546, W.629 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.546 Water bridges: A:S.545, A:S.545 NAG.12: 3 residues within 4Å: Chain A: Y.610, N.612, T.614 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.612, A:T.614, A:T.614 NAG.13: 5 residues within 4Å: Chain A: V.72, P.73, W.74, G.111, N.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.112 NAG.14: 2 residues within 4Å: Chain A: T.651, N.652 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.651 Hydrogen bonds: A:N.652 Water bridges: A:Q.757, A:Q.757 NAG.20: 3 residues within 4Å: Chain B: N.44, T.47 Ligands: NAG-NAG.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.44 NAG.21: 3 residues within 4Å: Chain B: L.52, Q.90, N.91 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.52 Water bridges: B:Q.90, B:N.91 NAG.22: 3 residues within 4Å: Chain B: Y.610, N.612, T.614 No protein-ligand interaction detected (PLIP) NAG.23: 5 residues within 4Å: Chain B: V.72, P.73, W.74, G.111, N.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.112

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 8 residues within 4Å: Chain A: R.162, V.587, L.590, P.591 Chain B: R.162, V.587, L.590, P.591 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.162, B:R.162, B:V.587 Water bridges: A:E.160, A:E.160, A:E.160, A:E.160, B:E.160 GOL.16: 7 residues within 4Å: Chain A: Q.36, Y.67, M.151, A.279, M.315, G.316, G.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.36 Water bridges: A:G.37, A:Y.320 GOL.17: 1 residues within 4Å: Chain A: W.493 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.493 GOL.18: 3 residues within 4Å: Chain A: A.516, K.520, W.543 No protein-ligand interaction detected (PLIP) GOL.24: 7 residues within 4Å: Chain B: D.684, V.691, P.692, L.695, L.721, G.722, L.723 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.684, B:P.692, B:L.721 Water bridges: B:L.723 GOL.25: 6 residues within 4Å: Chain B: Q.36, Y.67, M.151, M.315, G.316, G.317 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.36, B:Q.36 Water bridges: B:D.38 GOL.26: 8 residues within 4Å: Chain B: A.78, V.81, K.82, L.145, G.146, Y.360, N.361, A.362 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.82, B:L.145, B:N.361, B:A.362 Water bridges: B:G.146, B:P.359 GOL.27: 8 residues within 4Å: Chain B: Y.258, T.262, P.308, A.309, G.310, I.338, T.341, R.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.262, B:R.345, B:R.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuzawa, T. et al., Crystal structure and substrate recognition mechanism of Aspergillus oryzae isoprimeverose-producing enzyme. J.Struct.Biol. (2019)

Release Date

2018-11-07

Peptides

Isoprimeverose-producing enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoprimeverose-producing enzyme

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