MolNFT v1 · #80522 · protein
Crystal structure of a tryptophanyl-tRNA synthetase from encephalitozoon cuniculi bound to tryptophan
3TZE: “Crystal structure of a tryptophanyl-tRNA synthetase from encephalitozoon cuniculi bound to tryptophan”. X-ray diffraction, 2 ligands (TRP, K), 8 pockets (best druggability 0.82). MolNFT v1 #80522 on GenesisL1: 3D structure, binding…
- PDB
- 3TZE
- Type
- protein
- Length
- 699 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- O96771
- Ligands
- TRP, K
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 360 | 57% helix, 11% strand | O96771 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 339 | 59% helix, 12% strand | O96771 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
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 | 160 | 0.82 | 0.98 | 27 | empty |
| 2 | 326 | 0.68 | 0.82 | 45 | TRP |
| 3 | 246 | 0.62 | 0.81 | 36 | TRP |
| 4 | 162 | 0.48 | 0.77 | 19 | empty |
| 5 | 101 | 0.37 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1488 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3TZE · Crystal structure of a tryptophanyl-tRNA synthetase from Encephalitozoon cuniculi bound… · the same entry in another collection · chain A against A, TM-score 1.00
- O96771 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (O96771) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O96771
- Elsewhere: RCSB PDB 3TZE · PDBe 3TZE · UniProt O96771
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