SMTL ID : 5nit.1

Glucose oxidase mutant A2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-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.1: 3 residues within 4Å: Chain A: A.84, T.85, N.87 No protein-ligand interaction detected (PLIP)

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

FAD.2: 38 residues within 4Å: Chain A: G.24, 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, Y.513, D.546, G.547, H.557, V.558, M.559, F.562 Ligands: OXY.3 30 PLIP interactions: 30 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:S.101, A:S.101, A:T.102, A:N.105, A:G.106, A:T.108, A:T.108, A:V.248, A:V.248, A:G.547, A:H.557, A:V.558, A:M.559 Water bridges: A:G.26, A:G.29, A:S.101, A:S.289, A:S.289, A:T.560 pi-Cation interactions: A:H.514, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.514, A:H.557, A:V.558

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

NAG.4: 4 residues within 4Å: Chain A: Y.157, N.159, S.161, C.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.157, A:N.159 NAG.5: 5 residues within 4Å: Chain A: N.353, S.360, E.361, H.364, N.405 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.353, A:S.360 Water bridges: A:N.353, A:H.364, A:N.405 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:A.389 Water bridges: A:N.386

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

DIO.7: 7 residues within 4Å: Chain A: R.111, W.131, V.134, A.135, S.138, T.560, V.561 Ligand excluded by PLIP DIO.8: 6 residues within 4Å: Chain A: A.153, A.154, Y.180, S.181, P.182, K.185 Ligand excluded by PLIP DIO.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DIO.10: 3 residues within 4Å: Chain A: H.113, G.205, D.206 Ligand excluded by PLIP DIO.11: 4 residues within 4Å: Chain A: P.182, K.185, A.186, A.477 Ligand excluded by PLIP DIO.12: 2 residues within 4Å: Chain A: T.388, L.391 Ligand excluded by PLIP DIO.13: 4 residues within 4Å: Chain A: E.79, T.80, V.81, F.446 Ligand excluded by PLIP DIO.14: 7 residues within 4Å: Chain A: N.86, Q.88, T.89, A.90, F.509, R.510, P.511 Ligand excluded by PLIP DIO.15: 5 residues within 4Å: Chain A: L.63, N.64, R.174, Q.345, D.414 Ligand excluded by PLIP DIO.16: 9 residues within 4Å: Chain A: R.111, W.131, A.135, L.139, S.161, C.162, G.203, C.204 Ligands: DIO.23 Ligand excluded by PLIP DIO.17: 5 residues within 4Å: Chain A: I.336, T.337, S.338, A.341, G.417 Ligand excluded by PLIP DIO.18: 4 residues within 4Å: Chain A: V.123, I.392, E.395, N.396 Ligand excluded by PLIP DIO.19: 1 residues within 4Å: Chain A: D.178 Ligand excluded by PLIP DIO.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DIO.21: 2 residues within 4Å: Chain A: E.219, D.220 Ligand excluded by PLIP DIO.22: 6 residues within 4Å: Chain A: K.185, M.188, S.189, E.192, T.198, K.199 Ligand excluded by PLIP DIO.23: 4 residues within 4Å: Chain A: D.132, A.136, L.139 Ligands: DIO.16 Ligand excluded by PLIP DIO.24: 3 residues within 4Å: Chain A: T.160, S.161, H.163 Ligand excluded by PLIP

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

EPE.25: 4 residues within 4Å: Chain A: Q.255, K.304, D.313, T.314 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.314 Water bridges: A:T.314 Salt bridges: A:K.304, A:D.313, A:D.313

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