MolNFT v1 · #156271 · protein
Crystal structure of S1052D mutant of formylglycinamidine synthetase
6LYL · Phosphoribosylformylglycinamidine synthase: “Crystal structure of S1052D mutant of formylglycinamidine synthetase”. X-ray diffraction, 3 ligands (ADP, MG, SO4), 9 pockets (best druggability 0.85). MolNFT v1 #156271 on GenesisL1: 3D…
- PDB
- 6LYL
- Type
- protein
- Length
- 1,288 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
- 9 · 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 | 1288 | 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 · 23 copies · chains A
- GOL · Glycerol · additive · 9 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.85 | 0.96 | 45 | MG, ADP |
| 2 | 1002 | 0.83 | 0.84 | 95 | SO4 |
| 3 | 102 | 0.78 | 0.99 | 29 | empty |
| 4 | 274 | 0.78 | 0.90 | 36 | GOL |
| 5 | 1009 | 0.77 | 0.79 | 86 | SO4 |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6LYL · Crystal structure of S1052D 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 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 P74881
- Elsewhere: RCSB PDB 6LYL · PDBe 6LYL · UniProt P74881
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