Research workbench
Gamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus in complex with GDP and formate ion
Analyse Gamma subunit of the translation initiation factor 2 from Sulfolobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I5M
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Sulfolobus solfataricus
- Molecule
- Translation initiation factor 2 subunit gamma
- UniProt
- Q980A5
- Ligands
- GDP, MG, NA
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 subunit gamma | protein | 414 | 19% helix, 40% strand | Q980A5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- FMT · Formic acid · additive · 17 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.61 | 0.80 | 45 | FMT |
| 2 | 333 | 0.61 | 0.78 | 35 | FMT |
| 3 | 156 | 0.57 | 0.82 | 33 | GDP, FMT, MG |
| 4 | 296 | 0.56 | 0.76 | 32 | FMT |
| 5 | 76 | 0.35 | 0.76 | 14 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6I5M · Gamma subunit of the translation initiation factor 2 from sulfolobus solfataricus in… · 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 0.95
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 6I5M · PDBe 6I5M · UniProt Q980A5
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