MolNFT v1 · #48213 · protein
The structures of AIF2GAMMA subunit from the archaeon sulfolobus solfataricus in the GDP-bound form.
2PMD · Translation initiation factor 2 gamma subunit: “The structures of AIF2GAMMA subunit from the archaeon sulfolobus solfataricus in the GDP-bound form.”. X-ray diffraction, 3 ligands (PPV, GDP, GNP), 11 pockets (best druggability…
- PDB
- 2PMD
- Type
- protein
- Length
- 828 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 gamma subunit
- UniProt
- Q980A5
- Ligands
- PPV, GDP, GNP
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Translation initiation factor 2 gamma subunit | protein | 414 | 16% helix, 38% strand | Q980A5 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 6 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.73 | 0.79 | 85 | PPV |
| 2 | 335 | 0.70 | 0.83 | 47 | empty |
| 3 | 496 | 0.69 | 0.79 | 80 | GNP, PPV |
| 4 | 390 | 0.64 | 0.78 | 44 | empty |
| 5 | 344 | 0.61 | 0.78 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 621 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2PMD · The structures of aIF2gamma subunit from the archaeon Sulfolobus solfataricus in the… · 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 0.94
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 2PMD · PDBe 2PMD · UniProt Q980A5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.