SMTL ID : 3rja.1

Crystal structure of carbohydrate oxidase from Microdochium nivale in complex with substrate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 33 residues within 4Å: Chain A: F.29, A.65, K.66, S.67, G.68, G.69, H.70, S.71, Y.72, F.75, L.88, P.108, G.130, T.131, C.132, V.135, G.136, S.138, G.139, H.140, H.143, G.145, F.146, G.191, S.192, G.195, I.196, V.197, Q.314, Y.425, N.427, Y.428 Ligands: ABL.6 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:F.29, A:H.70, A:Y.72, A:V.135 Hydrogen bonds: A:A.65, A:S.67, A:G.68, A:G.69, A:H.70, A:S.71, A:F.75, A:G.76, A:T.131, A:G.136, A:G.136, A:S.138, A:G.139, A:H.140, A:F.146, A:F.146, A:S.192, A:V.197, A:V.197, A:Y.425, A:N.427, A:N.427, A:Y.428 Water bridges: A:G.69, A:Y.72, A:S.192, A:R.248, A:Y.465 pi-Stacking: A:H.140

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

NAG.2: 2 residues within 4Å: Chain A: N.222, S.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.225 Water bridges: A:K.221, A:N.222

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.114, D.309, I.311 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.114, A:D.309, A:D.309, H2O.2, H2O.4 ZN.4: 2 residues within 4Å: Chain A: D.306, H.307 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.306, A:H.307 ZN.5: 2 residues within 4Å: Chain A: E.231, D.235 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.231, A:D.235, A:D.235

2 x ABL: (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside(Non-covalent)

ABL.6: 15 residues within 4Å: Chain A: F.29, Y.72, T.131, C.132, R.248, Y.252, N.304, E.317, F.354, Q.356, Q.387, Y.389, R.391, Y.428 Ligands: FAD.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.72, A:Y.72, A:R.248, A:N.304, A:E.317, A:Q.356, A:Q.387, A:Y.389, A:R.391, A:R.391, A:Y.428 Water bridges: A:R.248 ABL.7: 9 residues within 4Å: Chain A: P.13, I.14, D.15, I.16, T.19, D.21, Y.22, Q.42 Ligands: CL.10 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.14, A:I.14, A:I.16, A:T.19, A:T.19, A:Y.22 Water bridges: A:Q.42, A:Q.42

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 6 residues within 4Å: Chain A: Q.44, R.90, M.91, I.92, D.93, E.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.44, A:R.90, A:I.92, A:D.93, A:E.107

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 2 residues within 4Å: Chain A: R.32, L.33 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.32, A:R.32, A:R.32 Salt bridges: A:R.32

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain A: T.19, A.20, D.21 Ligands: ABL.7 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: V.472, K.473 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: R.435, Y.464 Ligands: CL.13 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: R.435, Y.464, R.470 Ligands: CL.12 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duskova, J. et al., Crystal structure and kinetic studies of carbohydrate oxidase from Microdochium nivale. To be Published

Release Date

2012-04-18

Peptides

Carbohydrate oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Carbohydrate oxidase

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