MolNFT v1 · #28566 · protein
Crystal structure of tryptophanyl tRNA synthetase II from deinococcus radiodurans in complex with 5-hydroxy tryptophan.
1YIA · Tryptophanyl-tRNA synthetase: “Crystal structure of tryptophanyl tRNA synthetase II from deinococcus radiodurans in complex with 5-hydroxy…”. X-ray diffraction, 1 ligand (HRP), 6 pockets (best druggability 0.80). MolNFT v1 #28566 on…
- PDB
- 1YIA
- Type
- protein
- Length
- 993 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- Q9RVD6
- Ligands
- HRP
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 331 | 55% helix, 9% strand | Q9RVD6 |
Ligands and binding sites
- HRP · 5-hydroxy-L-tryptophan · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.80 | 0.84 | 64 | HRP |
| 2 | 803 | 0.76 | 0.80 | 58 | empty |
| 3 | 825 | 0.72 | 0.77 | 62 | empty |
| 4 | 56 | 0.69 | 0.97 | 23 | empty |
| 5 | 58 | 0.38 | 0.80 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2018 Ų buried · 27 hydrogen bonds · protein-protein
- B–A · 94 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1YIA · Crystal structure of tryptophanyl tRNA synthetase II from Deinococcus radiodurans in… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9RVD6 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase 2 (Q9RVD6) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q9RVD6
- Elsewhere: RCSB PDB 1YIA · PDBe 1YIA · UniProt Q9RVD6
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