MolNFT v1 · #105704 · protein
Structure of AIF2-gamma H97A variant from sulfolobus solfataricus bound to gdpnp
4RD2 · Translation initiation factor 2 subunit gamma: “Structure of AIF2-gamma H97A variant from sulfolobus solfataricus bound to gdpnp”. X-ray diffraction, 2 ligands (GNP, MG), 5 pockets (best druggability 0.56). MolNFT v1 #105704 on…
- PDB
- 4RD2
- 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
- GNP, MG
- Pockets
- 5 · 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
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.56 | 0.80 | 38 | empty |
| 2 | 258 | 0.55 | 0.77 | 35 | empty |
| 3 | 271 | 0.54 | 0.76 | 46 | GNP |
| 4 | 105 | 0.45 | 0.79 | 25 | GNP, MG |
| 5 | 57 | 0.28 | 0.74 | 13 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4RD2 · Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus bound to GDPNP · 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 4RD2 · PDBe 4RD2 · UniProt Q980A5
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