SMTL ID : 8jpz.1

The thermostability mutant Gox_M8 from Aspergillus niger

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: A.84, T.85, N.87, Y.507 Chain B: R.335, G.484, E.485, T.486, G.489, D.490, N.491 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.335, B:E.485, B:E.485, B:R.335, B:R.335, B:D.490, B:D.490 Hydrophobic interactions: B:T.486 NAG-NAG-BMA-MAN-MAN-MAN.2: 11 residues within 4Å: Chain A: R.335, G.484, E.485, T.486, I.487, G.489, D.490, N.491 Chain B: T.85, N.87, Y.507 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.335, A:E.485, A:E.485, A:R.335, A:R.335, A:D.490, A:D.490

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

FAD.3: 36 residues within 4Å: Chain A: G.24, G.26, L.27, T.28, I.47, E.48, S.49, Y.66, F.70, H.76, Y.78, R.93, G.95, N.96, G.97, G.100, S.101, T.102, N.105, G.106, G.107, T.108, Y.247, V.248, A.286, A.287, G.288, V.291, Y.513, D.546, G.547, H.557, V.558, M.559, F.562 Ligands: OXY.5 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:F.70, A:Y.513, A:Y.513 Hydrogen bonds: A:L.27, A:T.28, A:S.49, A:G.95, A:G.97, A:G.99, A:S.101, A:T.102, A:N.105, A:G.106, A:T.108, A:T.108, A:T.108, A:V.248, A:V.248, A:G.547, A:V.558, A:M.559 Water bridges: A:G.26, A:T.28, A:Y.78, A:S.101, A:S.289, A:S.289, A:T.560 pi-Cation interactions: A:H.514 FAD.12: 36 residues within 4Å: Chain B: G.24, G.25, G.26, L.27, T.28, I.47, E.48, S.49, Y.66, F.70, H.76, R.93, G.95, N.96, G.97, G.100, S.101, T.102, N.105, G.106, G.107, T.108, Y.247, V.248, A.286, A.287, G.288, V.291, Y.513, D.546, G.547, H.557, V.558, M.559, F.562 Ligands: OXY.14 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:F.70, B:Y.513, B:Y.513 Hydrogen bonds: B:G.25, B:L.27, B:T.28, B:S.49, B:G.95, B:G.97, B:G.99, B:G.100, B:S.101, B:T.102, B:N.105, B:G.106, B:T.108, B:T.108, B:T.108, B:V.248, B:V.248, B:G.547, B:V.558, B:M.559 Water bridges: B:G.26, B:G.29, B:Y.78, B:S.101, B:S.289, B:T.560 pi-Cation interactions: B:H.514, B:H.514

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 7 residues within 4Å: Chain A: E.503, Y.504, Y.507, H.508 Chain B: D.490, N.491 Ligands: EPE.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.508 Hydrogen bonds: B:N.491 EPE.13: 7 residues within 4Å: Chain A: D.490, N.491 Chain B: E.503, Y.504, Y.507, H.508 Ligands: EPE.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.490, A:N.491 Water bridges: B:N.491 Salt bridges: B:H.508

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.5: 4 residues within 4Å: Chain A: H.514, H.557, V.558 Ligands: FAD.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.558 OXY.14: 4 residues within 4Å: Chain B: H.514, H.557, V.558 Ligands: FAD.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.558

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

NAG.6: 6 residues within 4Å: Chain A: N.386, T.388, A.389, I.392, E.525, M.526 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.386, A:A.389 NAG.7: 5 residues within 4Å: Chain A: Y.157, N.159, S.161, C.162 Ligands: MPD.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.157 Water bridges: A:N.159, A:N.159, A:N.159 NAG.8: 4 residues within 4Å: Chain A: N.353, T.360, H.364, N.405 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.353, A:E.361 NAG.9: 2 residues within 4Å: Chain A: R.194, N.471 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.194 Water bridges: A:N.471 NAG.10: 2 residues within 4Å: Chain A: L.252, N.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.276 Water bridges: A:L.253 NAG.15: 4 residues within 4Å: Chain B: Y.157, N.159, S.161, C.162 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.161 Water bridges: B:N.159, B:N.159, B:N.159 NAG.16: 5 residues within 4Å: Chain B: N.353, T.360, E.361, H.364, N.405 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.361, B:E.361 NAG.17: 6 residues within 4Å: Chain B: N.386, T.388, A.389, I.392, E.525, M.526 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.386, B:A.389 Water bridges: B:N.386 NAG.18: 5 residues within 4Å: Chain B: S.254, N.256, T.258, R.261, V.263 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.254, B:N.256, B:T.258, B:T.258 Water bridges: B:N.256 NAG.19: 1 residues within 4Å: Chain B: N.276 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.276, B:N.276 NAG.20: 2 residues within 4Å: Chain B: R.194, N.471 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.194 Water bridges: B:N.471

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.11: 4 residues within 4Å: Chain A: W.131, S.161, C.204 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.204 Water bridges: A:D.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tu, T. et al., Revealing the pH-Dependent Activity Mechanism of a Ferrari Oxidoreductase Enzyme-Glucose Oxidase. To Be Published

Release Date

2023-12-20

Peptides

Glucose oxidase (Fragment): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucose oxidase (Fragment)