Research workbench
Catalytic mechanism of quinoprotein methanol dehydrogenase: a theoretical and X-ray crystallographic investigation
Analyse Catalytic mechanism of quinoprotein methanol dehydrogenase: a theoretical and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G72
- Type
- protein
- Length
- 1,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methanol dehydrogenase heavy subunit; Methanol dehydrogenase light subunit
- EC
- 1.1.99.8
- UniProt
- P38539, P38540
- Ligands
- PQQ, CA
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Methanol dehydrogenase heavy subunit (EC 1.1.99.8) | protein | 571 | 10% helix, 36% strand | P38539 |
| B, D | Methanol dehydrogenase light subunit (EC 1.1.99.8) | protein | 57 | 39% helix, 4% 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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.78 | 0.98 | 28 | CA, PQQ |
| 2 | 100 | 0.77 | 0.98 | 28 | CA, PQQ |
| 3 | 110 | 0.68 | 0.91 | 25 | empty |
| 4 | 111 | 0.66 | 0.90 | 24 | empty |
| 5 | 241 | 0.49 | 0.74 | 37 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1851 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1831 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1343 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1G72 · Catalytic mechanism of quinoprotein methanol dehydrogenase: a theoretical and X-ray… · 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 1G72 · PDBe 1G72 · UniProt P38539 · UniProt P38540
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.