MolNFT v1 · #13912 · protein
Crystal structure of methanol dehydrogenase from P. denitrificans
1LRW · Methanol dehydrogenase subunit 1: “Crystal structure of methanol dehydrogenase from P. denitrificans”. X-ray diffraction, 2 ligands (PQQ, CA), 12 pockets (best druggability 0.79). MolNFT v1 #13912 on GenesisL1: 3D structure, binding…
- PDB
- 1LRW
- Type
- protein
- Length
- 1,366 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
- P12293, P29898
- Ligands
- PQQ, CA
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Methanol dehydrogenase subunit 1 (EC 1.1.99.8) | protein | 600 | 10% helix, 35% strand | P12293 |
| B, D | Methanol dehydrogenase subunit 2 (EC 1.1.99.8) | protein | 83 | 36% helix, 2% strand | P29898 |
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 | 121 | 0.79 | 0.98 | 30 | CA, PQQ |
| 2 | 98 | 0.76 | 0.97 | 30 | CA, PQQ |
| 3 | 59 | 0.63 | 0.93 | 20 | empty |
| 4 | 377 | 0.61 | 0.77 | 57 | empty |
| 5 | 65 | 0.48 | 0.84 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2306 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1992 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1970 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1LRW · Crystal structure of methanol dehydrogenase from P. denitrificans · the same entry in another collection · chain D against D, TM-score 1.00
- P12293 · 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 0.99
- P29898 · AlphaFold monomer V2.0 prediction for methanol dehydrogenase [cytochrome C] subunit 2… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P12293
- Every structure of UniProt P29898
- Elsewhere: RCSB PDB 1LRW · PDBe 1LRW · UniProt P12293 · UniProt P29898
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