- Coordinates
- PDB Format
- 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
- 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)
- 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
AB
A
- Coordinates
- PDB Format
- 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
- 2 x BGC- XYS: alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose(Non-covalent)
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x CA: CALCIUM ION(Non-covalent)
- 12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 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
AB
A