Research workbench
Crystal structure of R1263A mutant of formylglycinamidine synthetase
Analyse Crystal structure of R1263A 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
- 6LYK
- Type
- protein
- Length
- 1,293 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, GLN, MG, SO4
- Pockets
- 10 · best druggability 0.86
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 | 1293 | 35% helix, 27% strand | P74881 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- GLN · Glutamine · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- SO4 · Sulfate ion · ion · 17 copies · chains A
- GOL · Glycerol · additive · 17 copies · chains A
- EDO · 1,2-ethanediol · additive · 15 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.86 | 0.97 | 52 | ADP, MG |
| 2 | 1022 | 0.83 | 0.84 | 88 | EDO, SO4, GOL |
| 3 | 283 | 0.79 | 0.91 | 38 | GOL |
| 4 | 122 | 0.79 | 0.98 | 32 | empty |
| 5 | 911 | 0.78 | 0.81 | 81 | EDO, SO4, GOL |
Compared structures
- 6LYK · Crystal Structure of R1263A 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 6LYK · PDBe 6LYK · UniProt P74881
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