MolNFT v1 · #14364 · protein
Binary complex of human glutathione-dependent formaldehyde dehydrogenase and 12-hydroxydodecanoic acid
1M6W: “Binary complex of human glutathione-dependent formaldehyde dehydrogenase and 12-hydroxydodecanoic acid”. X-ray diffraction, 4 ligands (12H, ZN, K), 7 pockets (best druggability 0.78). MolNFT v1 #14364 on GenesisL1: 3D structure…
- PDB
- 1M6W
- Type
- protein
- Length
- 746 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione-dependent formaldehyde dehydrogenase
- EC
- 1.1.1.1
- UniProt
- P11766
- Ligands
- 12H, ZN, K, PO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutathione-dependent formaldehyde dehydrogenase (EC 1.1.1.1) | protein | 373 | 31% helix, 26% strand | P11766 |
Ligands and binding sites
- 12H · 12-hydroxydodecanoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.78 | 0.81 | 69 | 12H |
| 2 | 484 | 0.75 | 0.83 | 53 | 12H |
| 3 | 472 | 0.67 | 0.79 | 53 | K, PO4 |
| 4 | 266 | 0.60 | 0.79 | 42 | PO4 |
| 5 | 63 | 0.36 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1632 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1M6W · Binary complex of Human glutathione-dependent formaldehyde dehydrogenase and… · the same entry in another collection · chain A against A, TM-score 1.00
- P11766 · AlphaFold monomer V2.0 prediction for alcohol dehydrogenase class-3 (P11766) · a predicted model of the same protein · chain B 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 P11766
- Elsewhere: RCSB PDB 1M6W · PDBe 1M6W · UniProt P11766
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