MolNFT v1 · #34335 · protein
Crystal structure of translation initiation factor AIF2BETAGAMMA heterodimer with GDP
2DCU · Translation initiation factor 2 gamma subunit: “Crystal structure of translation initiation factor AIF2BETAGAMMA heterodimer with GDP”. X-ray diffraction, 3 ligands (GDP, ZN, MG), 8 pockets (best druggability 0.66). MolNFT v1 #34335…
- PDB
- 2DCU
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 gamma subunit; Translation initiation factor 2 beta…
- UniProt
- Q8U082, Q8U3I5
- Ligands
- GDP, ZN, MG
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 gamma subunit | protein | 407 | 18% helix, 36% strand | Q8U082 |
| B | Translation initiation factor 2 beta subunit | protein | 137 | 34% helix, 13% strand | Q8U3I5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.66 | 0.94 | 16 | empty |
| 2 | 396 | 0.63 | 0.78 | 36 | empty |
| 3 | 58 | 0.60 | 0.91 | 21 | empty |
| 4 | 117 | 0.49 | 0.79 | 25 | empty |
| 5 | 106 | 0.42 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1580 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2DCU · Crystal structure of translation initiation factor aIF2betagamma heterodimer with GDP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8U082 · 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 0.87
- Q8U3I5 · AlphaFold monomer V2.0 prediction for translation initiation factor 2 subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.79
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 Q8U082
- Every structure of UniProt Q8U3I5
- Elsewhere: RCSB PDB 2DCU · PDBe 2DCU · UniProt Q8U082 · UniProt Q8U3I5
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