MolNFT v1 · #10579 · protein + RNA
Crystal structure of thermus thermophilus valyl-tRNA synthetase complexed with TRNA(VAL) and valyl-adenylate analogue
1IVS · TRNA (val): “Crystal structure of thermus thermophilus valyl-tRNA synthetase complexed with TRNA(VAL) and valyl-adenylate…”. X-ray diffraction, 1 ligand (VAA), 20 pockets (best druggability 0.83). MolNFT v1 #10579 on GenesisL1: 3D…
- PDB
- 1IVS
- Type
- protein + RNA
- Length
- 1,874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (val); Valyl-tRNA synthetase
- EC
- 6.1.1.9
- UniProt
- P96142
- Ligands
- VAA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | TRNA (val) | rna | 75 | — | — |
| A, B | Valyl-tRNA synthetase (EC 6.1.1.9) | protein | 862 | 44% helix, 16% strand | P96142 |
Ligands and binding sites
- VAA · N-[valinyl]-N'-[adenosyl]-diaminosufone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.83 | 0.90 | 56 | empty |
| 2 | 414 | 0.80 | 0.89 | 52 | empty |
| 3 | 341 | 0.79 | 0.89 | 38 | VAA |
| 4 | 327 | 0.78 | 0.89 | 40 | VAA |
| 5 | 492 | 0.77 | 0.85 | 42 | empty |
Interfaces
3 interfaces between chains.
- D–B · 2730 Ų buried · 49 hydrogen bonds · protein-nucleic
- C–A · 2700 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–B · 970 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1IVS · Crystal structure of thermus thermophilus valyl-tRNA synthetase complexed with TRNA(VAL)… · the same entry in another collection · chain C against C, TM-score 1.00
- P96142 · AlphaFold monomer V2.0 prediction for valine--tRNA ligase (P96142) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P96142
- Elsewhere: RCSB PDB 1IVS · PDBe 1IVS · UniProt P96142
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