MolNFT v1 · #30891 · protein
Crystal structure of methanol dehydrogenase from M. W3A1 (form C)
2AD6 · Methanol dehydrogenase subunit 1: “Crystal structure of methanol dehydrogenase from M. W3A1 (form C)”. X-ray diffraction, 2 ligands (PQQ, CA), 13 pockets (best druggability 0.69). MolNFT v1 #30891 on GenesisL1: 3D structure, binding…
- PDB
- 2AD6
- Type
- protein
- Length
- 1,280 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methanol dehydrogenase subunit 1; Methanol dehydrogenase subunit 2
- EC
- 1.1.99.8
- UniProt
- P38539, P38540
- Ligands
- PQQ, CA
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Methanol dehydrogenase subunit 1 (EC 1.1.99.8) | protein | 571 | 10% helix, 36% strand | P38539 |
| B, D | Methanol dehydrogenase subunit 2 (EC 1.1.99.8) | protein | 69 | 39% helix, 3% strand | P38540 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.69 | 0.97 | 18 | empty |
| 2 | 182 | 0.69 | 0.87 | 37 | CA, PQQ |
| 3 | 204 | 0.67 | 0.85 | 44 | CA, PQQ |
| 4 | 53 | 0.65 | 0.95 | 18 | empty |
| 5 | 164 | 0.48 | 0.77 | 30 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1904 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1894 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1347 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2AD6 · crystal structure of methanol dehydrogenase from M. W3A1 (form C) · the same entry in another collection · chain D against D, TM-score 1.00
- P38539 · AlphaFold monomer V2.0 prediction for methanol dehydrogenase [cytochrome C] subunit 1… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P38540 · AlphaFold monomer V2.0 prediction for methanol dehydrogenase [cytochrome C] subunit 2… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P38539
- Every structure of UniProt P38540
- Elsewhere: RCSB PDB 2AD6 · PDBe 2AD6 · UniProt P38539 · UniProt P38540
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