Research workbench
Crystal structure of D657A mutant of formylglycinamidine synthetase
Analyse Crystal structure of D657A mutant of formylglycinamidine synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LYM
- Type
- protein
- Length
- 1,281 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylformylglycinamidine synthase
- EC
- 6.3.5.3
- UniProt
- P74881
- Ligands
- ADP, MG, SO4
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylformylglycinamidine synthase (EC 6.3.5.3) | protein | 1281 | 35% helix, 27% strand | P74881 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- SO4 · Sulfate ion · ion · 18 copies · chains A
- GOL · Glycerol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.85 | 0.96 | 46 | ADP, MG |
| 2 | 877 | 0.82 | 0.84 | 81 | SO4 |
| 3 | 272 | 0.80 | 0.92 | 38 | empty |
| 4 | 123 | 0.78 | 0.97 | 31 | GOL |
| 5 | 1078 | 0.77 | 0.79 | 81 | SO4 |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6LYM · Crystal structure of D657A mutant of formylglycinamidine synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- P74881 · AlphaFold monomer V2.0 prediction for phosphoribosylformylglycinamidine synthase (P74881) · 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 P74881
- Elsewhere: RCSB PDB 6LYM · PDBe 6LYM · UniProt P74881
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