SMTL ID : 5niw.1

Glucose oxydase mutant A2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: A.84, T.85, N.86, N.87, Y.507 No protein-ligand interaction detected (PLIP)

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

FAD.2: 40 residues within 4Å: Chain A: G.24, G.25, G.26, L.27, V.28, I.47, E.48, S.49, Y.66, F.70, H.76, Y.78, R.93, G.95, N.96, G.97, G.99, G.100, S.101, T.102, N.105, G.106, G.107, T.108, Q.246, Y.247, V.248, A.286, A.287, G.288, V.291, I.295, Y.513, D.546, G.547, H.557, V.558, M.559, F.562 Ligands: OXY.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:F.70, A:Y.513, A:Y.513 Hydrogen bonds: A:G.25, A:L.27, A:V.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:G.29, A:Y.78, A:S.101, A:S.289, A:T.560 pi-Cation interactions: A:H.514

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 4 residues within 4Å: Chain A: H.514, H.557, V.558 Ligands: FAD.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.514, A:V.558

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

NAG.4: 6 residues within 4Å: Chain A: Y.157, N.159, S.161, C.162 Ligands: DIO.9, DIO.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.159 NAG.5: 3 residues within 4Å: Chain A: N.256, R.261, Q.540 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.261, A:Q.540 NAG.6: 5 residues within 4Å: Chain A: N.353, S.360, E.361, H.364, N.405 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.353, A:E.361 Water bridges: A:H.364 NAG.7: 5 residues within 4Å: Chain A: N.386, A.389, I.392, E.525, M.526 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.386, A:A.389 Water bridges: A:N.386 NAG.8: 3 residues within 4Å: Chain A: N.471, N.474, Y.494 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.474 Hydrogen bonds: A:N.471 Water bridges: A:R.194

12 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)(Non-functional Binders)

DIO.9: 9 residues within 4Å: Chain A: R.111, W.131, A.135, L.139, S.161, C.162, G.203, C.204 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) DIO.10: 4 residues within 4Å: Chain A: V.123, I.392, E.395, N.396 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.395 DIO.11: 5 residues within 4Å: Chain A: A.153, A.154, Y.180, S.181, P.182 No protein-ligand interaction detected (PLIP) DIO.12: 4 residues within 4Å: Chain A: H.218, D.220, V.222, R.228 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.228 DIO.13: 2 residues within 4Å: Chain A: E.219, D.220 No protein-ligand interaction detected (PLIP) DIO.14: 3 residues within 4Å: Chain A: T.388, L.391, E.395 No protein-ligand interaction detected (PLIP) DIO.15: 1 residues within 4Å: Ligands: NAG.4 No protein-ligand interaction detected (PLIP) DIO.16: 2 residues within 4Å: Chain A: Y.157, F.158 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.158 DIO.17: 9 residues within 4Å: Chain A: R.111, P.112, V.117, W.131, V.134, A.135, S.138, T.560, V.561 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.138 DIO.18: 4 residues within 4Å: Chain A: R.261, H.281, E.282, G.541 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.282, A:G.541 DIO.19: 2 residues within 4Å: Chain A: L.252, L.253 No protein-ligand interaction detected (PLIP) DIO.20: 6 residues within 4Å: Chain A: D.12, V.13, R.16, V.18, L.45, Q.241 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.21: 5 residues within 4Å: Chain A: G.71, S.72, S.73, D.75, H.76 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.77 PEG.22: 5 residues within 4Å: Chain A: D.55, G.57, P.58, E.61, D.62 No protein-ligand interaction detected (PLIP)

2 x P4C: O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL(Non-covalent)

P4C.23: 4 residues within 4Å: Chain A: K.271, G.272, K.439, D.440 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.271 P4C.24: 7 residues within 4Å: Chain A: E.79, T.80, V.81, T.89, L.437, H.445, F.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrovic, D. et al., Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase. ACS Catal (2017)

Release Date

2017-11-15

Peptides

Glucose oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucose oxidase