SMTL ID : 4mh1.1

Crystal structure and functional studies of quinoprotein L-sorbose dehydrogenase from Ketogulonicigenium vulgare Y25

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

2 x PQQ: PYRROLOQUINOLINE QUINONE(Non-covalent)

PQQ.1: 14 residues within 4Å: Chain B: Q.62, F.108, R.113, S.157, T.172, T.220, W.223, E.288, K.330, D.391, W.392, Y.467, Y.531 Ligands: CA.2 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.108, B:Y.531 Hydrogen bonds: B:Q.62, B:R.113, B:S.157, B:T.172, B:T.172, B:T.172, B:K.330, B:Y.467 Salt bridges: B:R.113, B:R.113 pi-Stacking: B:F.108, B:W.223, B:W.223 PQQ.3: 14 residues within 4Å: Chain D: Q.62, F.108, R.113, S.157, T.172, T.220, W.223, E.288, K.330, D.391, W.392, Y.467, Y.531 Ligands: CA.4 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.108, D:Y.531 Hydrogen bonds: D:Q.62, D:R.113, D:S.157, D:T.172, D:T.172, D:T.172, D:K.330, D:Y.467, D:Y.467 Salt bridges: D:R.113, D:R.113 pi-Stacking: D:F.108, D:W.223, D:W.223

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain B: W.223, E.288 Ligands: PQQ.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.288 CA.4: 3 residues within 4Å: Chain D: W.223, E.288 Ligands: PQQ.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, X. et al., Crystal structure of L-sorbose dehydrogenase, a pyrroloquinoline quinone-dependent enzyme with homodimeric assembly, from Ketogulonicigenium vulgare. Biotechnol.Lett. (2014)

Release Date

2014-07-23

Peptides

Sorbose dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Sorbose dehydrogenase