MolNFT v1 · #49398 · protein
Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states
2QMU · Translation initiation factor 2 gamma subunit: “Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and…”. X-ray diffraction, 3 ligands (GDP, ZN, PO4), 6 pockets (best druggability…
- PDB
- 2QMU
- Type
- protein
- Length
- 639 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, ZN, PO4
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 gamma subunit | protein | 414 | 16% helix, 36% strand | Q980A5 |
| B | Translation initiation factor 2 alpha subunit | protein | 93 | 34% helix, 25% strand | Q97Z79 |
| C | Translation initiation factor 2 beta subunit | protein | 132 | 34% helix, 18% strand | Q97W59 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A, C
- ZN · Zinc ion · metal · chains C
- 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.62 | 0.76 | 51 | PO4, GDP |
| 2 | 251 | 0.57 | 0.78 | 32 | empty |
| 3 | 194 | 0.52 | 0.78 | 30 | empty |
| 4 | 105 | 0.45 | 0.79 | 20 | empty |
| 5 | 87 | 0.36 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–C · 982 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 846 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2QMU · 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
- 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 0.96
- 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 0.94
- 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 0.82
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 2QMU · PDBe 2QMU · UniProt Q980A5 · UniProt Q97Z79 · UniProt Q97W59
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