SMTL ID : 7eap.1

Crystal structure of IpeA-XXXG complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

2 x BGC- BGC- BGC- BGC- XYS- XYS- XYS: alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-BGC-BGC-BGC-XYS-XYS-XYS.1: 20 residues within 4Å: Chain A: Q.36, E.45, Y.67, Y.70, 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, Q.489, W.493, A.494 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.165, A:R.165, A:K.198, A:H.199, A:H.199 Water bridges: A:Y.423 BGC-BGC-BGC-BGC-XYS-XYS-XYS.11: 20 residues within 4Å: Chain B: Q.36, E.45, Y.67, Y.70, 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, Q.489, W.493, A.494 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.165, B:R.165, B:K.198, B:H.199, B:H.199 Water bridges: B:Y.70

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

BGC-XYS.2: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.394, A:N.397, A:N.397, A:N.394, A:H.395 Water bridges: A:N.394, A:Y.634 BGC-XYS.12: 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.394, B:N.397, B:N.397, B:E.393, B:N.394, B:H.395, B:H.395 Water bridges: B:N.394

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 5 residues within 4Å: Chain A: W.458, R.487, N.497 Chain B: L.615, F.617 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain A: L.615, F.617 Chain B: W.458, R.487, N.497 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.3, H2O.7, H2O.10 CA.14: 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.25, H2O.26, H2O.30, H2O.33

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

NAG.5: 4 residues within 4Å: Chain A: N.44, T.46, T.47 Ligands: NAG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.44 NAG.6: 5 residues within 4Å: Chain A: N.51, T.53, G.54, W.57 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.51 NAG.7: 4 residues within 4Å: Chain A: D.86, Y.87, Q.90, N.91 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.90 Hydrogen bonds: A:N.91 Water bridges: A:Y.87 NAG.8: 5 residues within 4Å: Chain A: N.192, W.240, E.352, M.353, G.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.192 Water bridges: A:W.240, A:E.352 NAG.9: 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.10: 3 residues within 4Å: Chain A: Y.610, N.612, T.614 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.614, A:T.614 Water bridges: A:N.612, A:N.612 NAG.15: 4 residues within 4Å: Chain B: N.44, T.46, T.47 Ligands: NAG.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.44 Water bridges: B:T.47 NAG.16: 5 residues within 4Å: Chain B: N.51, T.53, G.54, W.57 Ligands: NAG.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.51 NAG.17: 4 residues within 4Å: Chain B: D.86, Y.87, Q.90, N.91 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.90 Hydrogen bonds: B:N.91 Water bridges: B:Y.87 NAG.18: 5 residues within 4Å: Chain B: N.192, W.240, E.352, M.353, G.354 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.192 Water bridges: B:W.240, B:E.352 NAG.19: 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.20: 3 residues within 4Å: Chain B: Y.610, N.612, T.614 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.614 Water bridges: B:N.612, B:N.612

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuzawa, T. et al., Structural basis for the catalytic mechanism of the glycoside hydrolase family 3 isoprimeverose-producing oligoxyloglucan hydrolase from Aspergillus oryzae. Febs Lett. (2022)

Release Date

2022-03-16

Peptides

Fn3_like domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Fn3_like domain-containing protein