Research workbench
Crystal structure of purl from thermus thermophilus
Analyse Crystal structure of purl from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VIU
- Type
- protein
- Length
- 703 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylformylglycinamidine synthase 2
- EC
- 6.3.5.3
- UniProt
- Q5SMH8
- Ligands
- ADP, MG, PO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylformylglycinamidine synthase 2 (EC 6.3.5.3) | protein | 703 | 38% helix, 26% strand | Q5SMH8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.81 | 0.87 | 50 | MG |
| 2 | 909 | 0.77 | 0.80 | 81 | ADP, PO4, PEG |
| 3 | 55 | 0.43 | 0.83 | 20 | empty |
| 4 | 89 | 0.37 | 0.76 | 22 | empty |
| 5 | 65 | 0.36 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 3VIU · Crystal structure of PurL from thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SMH8 · AlphaFold monomer V2.0 prediction for phosphoribosylformylglycinamidine synthase subunit… · 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 Q5SMH8
- Elsewhere: RCSB PDB 3VIU · PDBe 3VIU · UniProt Q5SMH8
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