MolNFT v1 · #55676 · protein
Crystal structure of gar synthetase from geobacillus kaustophilus
2YRX · Phosphoribosylglycinamide synthetase: “Crystal structure of gar synthetase from geobacillus kaustophilus”. X-ray diffraction, 2 ligands (AMP, PO4), 4 pockets (best druggability 0.60). MolNFT v1 #55676 on GenesisL1: 3D structure…
- PDB
- 2YRX
- Type
- protein
- Length
- 420 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylglycinamide synthetase
- EC
- 6.3.4.13
- UniProt
- Q5L3C7
- Ligands
- AMP, PO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylglycinamide synthetase (EC 6.3.4.13) | protein | 420 | 31% helix, 31% strand | Q5L3C7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.60 | 0.77 | 41 | AMP |
| 2 | 179 | 0.45 | 0.75 | 42 | PO4 |
| 3 | 94 | 0.36 | 0.74 | 19 | empty |
| 4 | 101 | 0.36 | 0.74 | 16 | empty |
Compared structures
- 2YRX · Crystal structure of GAR synthetase from Geobacillus kaustophilus · the same entry in another collection · 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 Q5L3C7
- Elsewhere: RCSB PDB 2YRX · PDBe 2YRX · UniProt Q5L3C7
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