SMTL ID : 5xm3.1

Crystal Structure of Methanol dehydrogenase from Methylophaga aminisulfidivorans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PQQ: PYRROLOQUINOLINE QUINONE(Non-covalent)

PQQ.1: 22 residues within 4Å: Chain A: E.86, C.134, C.135, V.138, R.140, T.190, S.205, G.206, A.207, E.208, T.272, W.274, N.292, D.334, A.336, R.362, N.425, Q.426, W.507, G.570, W.571 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.274, A:W.571 Hydrogen bonds: A:R.140, A:S.205, A:S.205, A:G.206, A:A.207, A:E.208, A:R.362, A:R.362, A:N.425, A:W.571 Water bridges: A:C.134, A:T.272, A:T.272 Salt bridges: A:R.140, A:R.140 pi-Stacking: A:W.274, A:W.274, A:W.274 PQQ.3: 22 residues within 4Å: Chain C: E.86, C.134, C.135, V.138, R.140, T.190, S.205, G.206, A.207, E.208, T.272, W.274, N.292, D.334, A.336, R.362, N.425, Q.426, W.507, G.570, W.571 Ligands: MG.4 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:W.274, C:W.571 Hydrogen bonds: C:R.140, C:T.190, C:S.205, C:S.205, C:G.206, C:A.207, C:E.208, C:T.272, C:R.362, C:R.362, C:N.425, C:W.571 Water bridges: C:C.134 Salt bridges: C:R.140, C:R.140 pi-Stacking: C:W.274, C:W.274, C:W.274

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.208, N.292, D.334 Ligands: PQQ.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.208, A:E.208 MG.4: 5 residues within 4Å: Chain C: E.208, N.292, D.334, A.336 Ligands: PQQ.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.208, C:E.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, T.P. et al., The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT. J. Microbiol. (2018)

Release Date

2018-03-21

Peptides

Glucose dehydrogenase: AC
Methanol dehydrogenase [cytochrome c] subunit 2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Glucose dehydrogenase

Methanol dehydrogenase [cytochrome c] subunit 2