SMTL ID : 5yqs.1

Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

6 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.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.57 NAG-NAG.2: 4 residues within 4Å: Chain A: S.190, N.192, M.353, G.354 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: W.458, R.487, N.497 Chain B: L.615, F.617 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.458 NAG-NAG.7: 3 residues within 4Å: Chain B: N.51, G.54, W.57 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: S.190, N.192, M.353, G.354 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 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

4 x BGC- XYS: alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose(Non-covalent)

BGC-XYS.4: 17 residues within 4Å: Chain A: Q.36, Y.67, E.103, M.151, R.165, K.198, H.199, M.243, Y.246, D.278, A.279, M.315, G.316, G.317, Y.423, E.502 Ligands: BGC.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.165, A:R.165, A:K.198, A:H.199, A:H.199, A:Y.246, A:Y.246, A:Q.36, A:Q.36, A:G.316, A:G.316 Water bridges: A:E.103, A:E.103 BGC-XYS.6: 6 residues within 4Å: Chain A: V.72, P.73, W.74, G.111, N.112, N.369 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.74, A:N.112, A:N.369, A:N.112 BGC-XYS.10: 16 residues within 4Å: Chain B: Q.36, Y.67, E.103, M.151, R.165, K.198, H.199, M.243, Y.246, D.278, A.279, M.315, G.316, G.317, Y.423, E.502 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.165, B:R.165, B:K.198, B:K.198, B:H.199, B:H.199, B:Y.246, B:Y.423, B:Q.36, B:Q.36, B:G.316, B:G.316 BGC-XYS.12: 6 residues within 4Å: Chain B: P.71, V.72, P.73, W.74, N.112, N.369 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.74, B:N.112, B:N.369

2 x GLC- XYS: alpha-D-xylopyranose-(1-6)-alpha-D-glucopyranose(Non-covalent)

GLC-XYS.5: 10 residues within 4Å: Chain A: L.391, E.393, N.394, H.395, N.397, K.636, S.637, Y.638, S.639, S.640 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.394, A:H.395, A:N.394, A:N.397, A:Y.638 GLC-XYS.11: 10 residues within 4Å: Chain B: L.391, E.393, N.394, H.395, N.397, K.636, S.637, Y.638, S.639, S.640 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.393, B:N.394, B:H.395, B:N.394, B:N.397, B:Y.638 Water bridges: B:N.394

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

NAG.13: 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.14: 4 residues within 4Å: Chain A: L.52, Y.87, Q.90, N.91 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.52, A:Y.87 NAG.15: 4 residues within 4Å: Chain A: P.542, S.545, N.546, W.629 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.546 NAG.16: 2 residues within 4Å: Chain A: N.612, T.614 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.612, A:T.614, A:T.614 NAG.17: 2 residues within 4Å: Chain A: T.651, N.652 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.652 NAG.20: 4 residues within 4Å: Chain B: N.44, T.46, T.47, E.49 No protein-ligand interaction detected (PLIP) NAG.21: 3 residues within 4Å: Chain B: L.52, Q.90, N.91 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.52 NAG.22: 4 residues within 4Å: Chain B: P.542, S.545, N.546, W.629 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.546 NAG.23: 2 residues within 4Å: Chain B: N.612, T.614 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.614

2 x CA: CALCIUM ION(Non-covalent)

CA.18: 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.5 CA.24: 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.12, H2O.13, H2O.14, H2O.14

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.19: 4 residues within 4Å: Chain A: Y.246, W.493 Ligands: BGC-XYS.4, BGC-XYS.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.246, A:Y.246 Water bridges: A:Q.489, A:E.502

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

2018-11-14

Peptides

Isoprimeverose-producing enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoprimeverose-producing enzyme

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