SMTL ID : 7o6z.1

Structure of a neodymium-containing, XoxF1-type methanol dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ND: Neodymium Ion(Non-covalent)

ND.1: 5 residues within 4Å: Chain A: E.204, N.290, D.345, D.347 Ligands: MOH.2 No protein-ligand interaction detected (PLIP) ND.4: 6 residues within 4Å: Chain B: E.204, N.290, D.345, D.347 Ligands: PQQ.3, MOH.5 No protein-ligand interaction detected (PLIP)

2 x MOH: METHANOL(Non-functional Binders)

MOH.2: 7 residues within 4Å: Chain A: C.137, E.204, W.294, D.345, W.576, L.594 Ligands: ND.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.372 MOH.5: 8 residues within 4Å: Chain B: C.137, E.204, W.294, D.345, W.576, L.594 Ligands: PQQ.3, ND.4 No protein-ligand interaction detected (PLIP)

1 x PQQ: PYRROLOQUINOLINE QUINONE(Non-covalent)

PQQ.3: 22 residues within 4Å: Chain B: E.86, C.136, C.137, V.140, R.142, T.186, G.201, G.202, D.203, E.204, W.272, N.290, D.345, D.347, R.372, D.434, Q.435, W.512, G.575, W.576 Ligands: ND.4, MOH.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.576 Hydrogen bonds: B:R.142, B:G.202, B:D.203, B:D.203, B:R.372, B:R.372, B:W.576 Salt bridges: B:R.142, B:R.142 pi-Stacking: B:W.272, B:W.272, B:W.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmitz, R.A. et al., Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase. Mbio (2021)

Release Date

2021-09-01

Peptides

Methanol dehydrogenase (Cytochrome c) subunit 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methanol dehydrogenase (Cytochrome c) subunit 1