MolNFT v1 · #106807 · protein
The crystal structure of methanol dehydrogenase from methylococcus capsulatus (bath)
4TQO · Methanol dehydrogenase protein, large subunit: “The crystal structure of methanol dehydrogenase from methylococcus capsulatus (bath)”. X-ray diffraction, 2 ligands (PQQ, CA), 20 pockets (best druggability 0.80). MolNFT v1 #106807 on…
- PDB
- 4TQO
- Type
- protein
- Length
- 5,156 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methanol dehydrogenase protein, large subunit; Methanol dehydrogenase, small subunit
- UniProt
- Q60AR6, Q60AR3
- Ligands
- PQQ, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D, E, F, G, H | Methanol dehydrogenase protein, large subunit | protein | 573 | 10% helix, 37% strand | Q60AR6 |
| I, J, K, L | Methanol dehydrogenase, small subunit | protein | 71 | 42% helix, 3% strand | Q60AR3 |
| M, N, O, P | Methanol dehydrogenase, small subunit | protein | 72 | 42% helix, 3% strand | Q60AR3 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 8 copies · chains B, A, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains B, A, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.80 | 0.98 | 29 | CA, PQQ |
| 2 | 118 | 0.80 | 0.98 | 30 | CA, PQQ |
| 3 | 119 | 0.80 | 0.98 | 32 | CA, PQQ |
| 4 | 114 | 0.79 | 0.98 | 30 | CA, PQQ |
| 5 | 125 | 0.79 | 0.97 | 30 | CA, PQQ |
Interfaces
20 interfaces between chains.
- E–M · 2057 Ų buried · 32 hydrogen bonds · protein-protein
- D–L · 2040 Ų buried · 31 hydrogen bonds · protein-protein
- H–P · 2029 Ų buried · 31 hydrogen bonds · protein-protein
- C–K · 2028 Ų buried · 29 hydrogen bonds · protein-protein
- G–O · 2021 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4TQO · The crystal structure of methanol dehydrogenase from Methylococcus capsulatus (Bath) · the same entry in another collection · chain B against B, 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 Q60AR6
- Every structure of UniProt Q60AR3
- Elsewhere: RCSB PDB 4TQO · PDBe 4TQO · UniProt Q60AR6 · UniProt Q60AR3
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