MolNFT v1 · #148923 · protein
Europium-containing methanol dehydrogenase
6FKW: “Europium-containing methanol dehydrogenase”. X-ray diffraction, 2 ligands (PQQ, EU), 19 pockets (best druggability 0.76). MolNFT v1 #148923 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FKW
- Type
- protein
- Length
- 2,304 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methanol dehydrogenase
- EC
- 1.1.2.7, 1.1.2.8
- UniProt
- I0JWN7
- Ligands
- PQQ, EU
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Methanol dehydrogenase (EC 1.1.2.7, 1.1.2.8) | protein | 576 | 11% helix, 36% strand | I0JWN7 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 4 copies · chains A, B, C, D
- EU · Europium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.76 | 0.98 | 30 | PQQ |
| 2 | 87 | 0.76 | 0.98 | 29 | PQQ |
| 3 | 621 | 0.75 | 0.81 | 50 | empty |
| 4 | 988 | 0.74 | 0.77 | 105 | empty |
| 5 | 166 | 0.69 | 0.88 | 40 | PQQ |
Interfaces
5 interfaces between chains.
- B–D · 1114 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1109 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 575 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 398 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6FKW · Europium-containing methanol dehydrogenase · 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 I0JWN7
- Elsewhere: RCSB PDB 6FKW · PDBe 6FKW · UniProt I0JWN7
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