Research workbench
Crystal structure of methanol dehydrogenase from hyphomicrobium denitrificans
Analyse Crystal structure of methanol dehydrogenase from hyphomicrobium denitrificans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D0V
- Type
- protein
- Length
- 1,997 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methanol dehydrogenase large subunit; Methanol dehydrogenase small subunit
- EC
- 1.1.99.8
- UniProt
- Q4AE26, Q4AE23
- Ligands
- PQQ, CA
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Methanol dehydrogenase large subunit (EC 1.1.99.8) | protein | 597 | 11% helix, 36% strand | Q4AE26 |
| B, J | Methanol dehydrogenase small subunit (EC 1.1.99.8) | protein | 70 | 39% helix, 0% strand | Q4AE23 |
| E | Methanol dehydrogenase small subunit (EC 1.1.99.8) | protein | 68 | 40% helix, 3% strand | Q4AE23 |
| I | Methanol dehydrogenase large subunit (EC 1.1.99.8) | protein | 595 | 10% helix, 36% strand | Q4AE26 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 3 copies · chains A, D, I
- CA · Calcium ion · metal · 3 copies · chains A, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.79 | 0.99 | 29 | CA, PQQ |
| 2 | 96 | 0.78 | 0.98 | 29 | PQQ |
| 3 | 1054 | 0.78 | 0.80 | 93 | empty |
| 4 | 92 | 0.77 | 0.98 | 29 | PQQ |
| 5 | 429 | 0.57 | 0.74 | 58 | empty |
Interfaces
5 interfaces between chains.
- D–I · 2306 Ų buried · 53 hydrogen bonds · protein-protein
- I–J · 2054 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2010 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1962 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 376 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 2D0V · Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans · 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 Q4AE26
- Every structure of UniProt Q4AE23
- Elsewhere: RCSB PDB 2D0V · PDBe 2D0V · UniProt Q4AE26 · UniProt Q4AE23
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