Research workbench
Crystal structure analysis of glutathione-dependent formaldehyde- activating enzyme (gfa)
Analyse Crystal structure analysis of glutathione-dependent formaldehyde- activating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XA8
- Type
- protein
- Length
- 780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione-dependent formaldehyde-activating enzyme
- EC
- 4.4.-.-
- UniProt
- Q51669
- Ligands
- GSH, ZN, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutathione-dependent formaldehyde-activating enzyme (EC 4.4.-.-) | protein | 196 | 23% helix, 25% strand | Q51669 |
| C, D | Glutathione-dependent formaldehyde-activating enzyme (EC 4.4.-.-) | protein | 194 | 23% helix, 25% strand | Q51669 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.70 | 0.78 | 68 | GSH, GOL |
| 2 | 503 | 0.68 | 0.78 | 68 | GSH |
| 3 | 90 | 0.49 | 0.83 | 18 | empty |
| 4 | 80 | 0.48 | 0.83 | 19 | empty |
| 5 | 78 | 0.48 | 0.83 | 18 | SO4 |
Interfaces
3 interfaces between chains.
- A–D · 852 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 852 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 113 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1XA8 · Crystal Structure Analysis of Glutathione-dependent formaldehyde-activating enzyme (Gfa) · the same entry in another collection · chain D against D, TM-score 1.00
- Q51669 · AlphaFold monomer V2.0 prediction for glutathione-dependent formaldehyde-activating… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q51669
- Elsewhere: RCSB PDB 1XA8 · PDBe 1XA8 · UniProt Q51669
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