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Crystal structure of phosphoribosylformylglycinamidine synthase II (TM1246) from thermotoga maritima at 2.15 a resolution
Analyse Crystal structure of phosphoribosylformylglycinamidine synthase II (TM1246)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VK3
- Type
- protein
- Length
- 586 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylformylglycinamidine synthase II
- EC
- 6.3.5.3
- UniProt
- Q9X0X3
- Ligands
- CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylformylglycinamidine synthase II (EC 6.3.5.3) | protein | 586 | 35% helix, 28% strand | Q9X0X3 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.78 | 0.80 | 85 | empty |
| 2 | 215 | 0.72 | 0.88 | 40 | empty |
| 3 | 78 | 0.46 | 0.82 | 21 | empty |
| 4 | 66 | 0.33 | 0.76 | 14 | CL |
| 5 | 59 | 0.32 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 1VK3 · Crystal structure of Phosphoribosylformylglycinamidine synthase II (TM1246) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X0X3 · AlphaFold monomer V2.0 prediction for phosphoribosylformylglycinamidine synthase subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9X0X3
- Elsewhere: RCSB PDB 1VK3 · PDBe 1VK3 · UniProt Q9X0X3
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