Research workbench
Lanthanide-dependent methanol dehydrogenase xoxf from methylobacterium extorquens, in complex with lanthanum and pyrroloquinoline quinone
Analyse Lanthanide-dependent methanol dehydrogenase xoxf from methylobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OC6
- Type
- protein
- Length
- 1,158 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lanthanide-dependent methanol dehydrogenase xoxf
- UniProt
- C5B120
- Ligands
- PQQ, LA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lanthanide-dependent methanol dehydrogenase xoxf | protein | 579 | 9% helix, 37% strand | C5B120 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 2 copies · chains A, B
- LA · Lanthanum (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.77 | 0.98 | 29 | LA, PQQ |
| 2 | 192 | 0.66 | 0.85 | 43 | PQQ |
| 3 | 138 | 0.46 | 0.77 | 28 | empty |
| 4 | 134 | 0.46 | 0.77 | 29 | empty |
| 5 | 188 | 0.45 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1193 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6OC6 · Lanthanide-dependent methanol dehydrogenase XoxF from Methylobacterium extorquens, in… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt C5B120
- Elsewhere: RCSB PDB 6OC6 · PDBe 6OC6 · UniProt C5B120
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