SMTL ID : 3das.1

Structure of the PQQ-bound form of Aldose Sugar Dehydrogenase (Adh) from Streptomyces coelicolor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x ARA: alpha-L-arabinopyranose(Non-covalent)

ARA.1: 6 residues within 4Å: Chain A: K.212, R.214, L.290, K.291, G.292 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.212, A:R.214, A:G.292 Salt bridges: A:K.291 ARA.2: 6 residues within 4Å: Chain A: D.261, R.281, G.282, E.283, R.284, E.304 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.281, A:R.284 Salt bridges: A:R.284

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: E.227, Y.237 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.227, A:Y.237, H2O.1, H2O.1, H2O.2 CA.4: 4 residues within 4Å: Chain A: R.202, G.221, Q.222 Ligands: PQQ.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.221, A:Q.222, H2O.1, H2O.1

1 x PQQ: PYRROLOQUINOLINE QUINONE(Non-covalent)

PQQ.5: 16 residues within 4Å: Chain A: E.79, H.140, R.202, N.203, Q.205, F.220, G.221, Q.222, T.260, S.264, L.280, R.281, R.309, R.311, R.331 Ligands: CA.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:R.202, A:R.202, A:N.203, A:Q.205, A:Q.205, A:S.264, A:R.281, A:R.331 Water bridges: A:R.50, A:E.79, A:G.221, A:T.260, A:R.281, A:R.309, A:R.311, A:R.311 Salt bridges: A:R.281, A:R.309, A:R.311, A:R.331, A:R.331 pi-Stacking: A:F.220, A:F.220

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: V.21 Ligands: EDO.7, EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.21 Water bridges: A:S.20 EDO.7: 6 residues within 4Å: Chain A: G.19, S.20, V.21, F.302 Ligands: EDO.6, EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.21, A:V.21 Water bridges: A:G.19 EDO.8: 4 residues within 4Å: Chain A: Q.300, A.301, F.302 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.300, A:A.301 EDO.9: 4 residues within 4Å: Chain A: A.301, F.302 Ligands: EDO.7, EDO.8 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain A: K.22 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain A: D.210, R.214, F.216, Y.270, L.290, G.292 Ligands: ARA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.210, A:D.210, A:R.214 Water bridges: A:D.211, A:G.273 EDO.12: 2 residues within 4Å: Chain A: H.252, D.253 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.230, A:K.232, A:T.293 EDO.13: 6 residues within 4Å: Chain A: P.185, A.186, P.187, G.188, N.189, G.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.186, A:G.188, A:G.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Southall, S.M. et al., Structural and Enzymatic Characterization of a Thermostable PQQ-dependent Soluble Aldose Sugar Dehydrogenase. To be Published

Release Date

2009-06-02

Peptides

Putative oxidoreductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative oxidoreductase