Research workbench
Xenon trapping and statistical coupling analysis uncover regions important for structure and function of multidomain protein stpurl
Analyse Xenon trapping and statistical coupling analysis uncover regions important for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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