SMTL ID : 4h7u.1

Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: S.340, K.343, N.344, S.550, W.551 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.550

1 x FED: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(4aR)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl dihydrogen diphosphate (non-preferred name)(Covalent)

FED.2: 38 residues within 4Å: Chain A: G.47, G.48, G.49, T.50, A.51, I.70, E.71, A.72, W.99, P.117, R.118, A.119, K.120, I.121, G.124, C.125, S.126, H.128, N.129, G.130, M.131, V.132, T.266, L.267, V.268, A.306, G.307, G.308, A.311, I.315, V.536, H.537, D.570, A.571, H.581, T.582, Q.583, V.586 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:V.536 Hydrogen bonds: A:G.48, A:T.50, A:T.50, A:T.50, A:A.51, A:A.72, A:A.119, A:I.121, A:G.123, A:C.125, A:N.129, A:G.130, A:V.132, A:V.132, A:V.268, A:V.268, A:H.537, A:A.571, A:T.582, A:Q.583, A:Q.583 Water bridges: A:G.49, A:G.52, A:R.118, A:R.118, A:A.119, A:T.134, A:V.309, A:V.309, A:H.581

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

NAG.3: 8 residues within 4Å: Chain A: G.94, S.95, P.96, D.98, W.99, N.100, K.120, Y.471 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.120 Hydrogen bonds: A:D.98, A:N.100 Water bridges: A:P.96, A:D.98

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain A: R.112, S.113, L.114, P.431, K.432 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.113, A:K.432 Water bridges: A:S.113, A:D.115, A:D.115, A:K.432, A:Q.433 Salt bridges: A:R.112, A:K.432

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, T.C. et al., The 1.6 A crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate. Plos One (2013)

Release Date

2013-08-07

Peptides

Pyranose dehydrogenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pyranose dehydrogenase