Research workbench
Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states
Analyse Structure of an archaeal heterotrimeric initiation factor 2 reveals a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QN6
- Type
- protein
- Length
- 501 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 gamma subunit; Translation initiation factor 2 alpha…
- UniProt
- Q980A5, Q97Z79, Q97W59
- Ligands
- GDP, MG
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 gamma subunit | protein | 393 | 19% helix, 41% strand | Q980A5 |
| B | Translation initiation factor 2 alpha subunit | protein | 90 | 41% helix, 36% strand | Q97Z79 |
| C | Translation initiation factor 2 beta subunit | protein | 18 | 67% helix, 0% strand | Q97W59 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.51 | 0.75 | 33 | empty |
| 2 | 173 | 0.48 | 0.76 | 27 | empty |
| 3 | 122 | 0.39 | 0.75 | 18 | empty |
| 4 | 67 | 0.38 | 0.79 | 17 | empty |
| 5 | 57 | 0.35 | 0.78 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 872 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 856 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2QN6 · Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97Z79 · AlphaFold monomer V2.0 prediction for translation initiation factor 2 subunit alpha… · a predicted model of the same protein · chain B against A, TM-score 0.97
- 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 0.93
- Q97W59 · AlphaFold monomer V2.0 prediction for translation initiation factor 2 subunit beta… · a predicted model of the same protein · chain C against A, TM-score 0.74
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
- Every structure of UniProt Q97Z79
- Every structure of UniProt Q97W59
- Elsewhere: RCSB PDB 2QN6 · PDBe 2QN6 · UniProt Q980A5 · UniProt Q97Z79 · UniProt Q97W59
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