MolNFT v1 · #76703 · protein + RNA
Recognition of the methionylated initiator tRNA by the translation initiation factor 2 in archaea
3QSY · Translation initiation factor 2 subunit gamma: “Recognition of the methionylated initiator tRNA by the translation initiation factor 2 in archaea”. X-ray diffraction, 2 ligands (MET, GNP), 16 pockets (best druggability 0.88). MolNFT…
- PDB
- 3QSY
- Type
- protein + RNA
- Length
- 581 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 subunit gamma; Translation initiation factor 2 subunit…
- UniProt
- Q980A5, Q97Z79
- Ligands
- MET, GNP
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 subunit gamma | protein | 415 | 9% helix, 18% strand | Q980A5 |
| B | Translation initiation factor 2 subunit alpha | protein | 89 | 38% helix, 26% strand | Q97Z79 |
| D | TRNA | rna | 77 | — | — |
Ligands and binding sites
- MET · Methionine · ligand · chains A, D
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.88 | 0.90 | 130 | empty |
| 2 | 461 | 0.78 | 0.86 | 57 | empty |
| 3 | 457 | 0.77 | 0.85 | 46 | empty |
| 4 | 603 | 0.71 | 0.80 | 31 | empty |
| 5 | 103 | 0.68 | 0.91 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1691 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 484 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 249 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3QSY · Recognition of the methionylated initiator tRNA by the translation initiation factor 2 in… · 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 0.74
- 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 0.70
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
- Elsewhere: RCSB PDB 3QSY · PDBe 3QSY · UniProt Q980A5 · UniProt Q97Z79
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