Research workbench
Ternary complex of human glutathione-dependent formaldehyde dehydrogenase with NAD+ and dodecanoic acid
Analyse Ternary complex of human glutathione-dependent formaldehyde dehydrogenase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MA0
- 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
- NAD, DAO, ZN, K, PO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutathione-dependent formaldehyde dehydrogenase (EC 1.1.1.1) | protein | 373 | 30% helix, 26% strand | P11766 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- DAO · Lauric 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 · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.79 | 0.81 | 84 | NAD, DAO |
| 2 | 1092 | 0.78 | 0.80 | 81 | NAD, DAO |
| 3 | 473 | 0.68 | 0.79 | 56 | PO4 |
| 4 | 75 | 0.37 | 0.77 | 13 | empty |
| 5 | 56 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1655 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1MA0 · Ternary complex of Human glutathione-dependent formaldehyde dehydrogenase with NAD+ 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 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 P11766
- Elsewhere: RCSB PDB 1MA0 · PDBe 1MA0 · UniProt P11766
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