Research workbench
Structure of AIF2-gamma H97A variant from sulfolobus solfataricus bound to GDP and pi
Analyse Structure of AIF2-gamma H97A variant from sulfolobus solfataricus bound to GDP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RD3
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 subunit gamma
- UniProt
- Q980A5
- Ligands
- GDP, MG, PO4
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 subunit gamma | protein | 414 | 19% helix, 39% strand | Q980A5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 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 | 278 | 0.56 | 0.77 | 35 | empty |
| 2 | 239 | 0.51 | 0.76 | 43 | GDP |
| 3 | 63 | 0.46 | 0.84 | 18 | empty |
| 4 | 80 | 0.44 | 0.81 | 20 | PO4, GDP, MG |
| 5 | 90 | 0.37 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4RD3 · Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus bound to GDP and Pi · the same entry in another collection · chain A against A, TM-score 1.00
- Q980A5 · AlphaFold monomer V2.0 prediction for translation initiation factor 2 subunit gamma… · 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 Q980A5
- Elsewhere: RCSB PDB 4RD3 · PDBe 4RD3 · UniProt Q980A5
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