MolNFT v1 · #98359 · protein
Xenon trapping and statistical coupling analysis uncover regions important for structure and function of multidomain protein stpurl
4L78 · Phosphoribosylformylglycinamidine synthase: “Xenon trapping and statistical coupling analysis uncover regions important for structure and function of…”. X-ray diffraction, 6 ligands (ADP, MG, MN), 9 pockets (best druggability 0.86).…
- PDB
- 4L78
- Type
- protein
- Length
- 1,285 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, MN, SO4, XE, CL
- Pockets
- 9 · 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 | 1285 | 35% helix, 27% strand | P74881 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 12 copies · chains A
- XE · Xenon · ion · 5 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- ACT · Acetate ion · 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 | 284 | 0.86 | 0.97 | 45 | ADP, MG |
| 2 | 1019 | 0.83 | 0.84 | 98 | SO4 |
| 3 | 288 | 0.79 | 0.91 | 38 | empty |
| 4 | 111 | 0.78 | 0.98 | 33 | empty |
| 5 | 1042 | 0.78 | 0.80 | 77 | SO4, CL |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4L78 · Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important for Structure… · 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 4L78 · PDBe 4L78 · UniProt P74881
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