MolNFT v1 · #68491 · protein
Crystal structure of pyrococcus horikoshii tryptophanyl-tRNA synthetase in complex with trpamp
3JXE: “Crystal structure of pyrococcus horikoshii tryptophanyl-tRNA synthetase in complex with trpamp”. X-ray diffraction, 2 ligands (TYM, SO4), 12 pockets (best druggability 0.76). MolNFT v1 #68491 on GenesisL1: 3D structure, binding…
- PDB
- 3JXE
- Type
- protein
- Length
- 724 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
- O59584
- Ligands
- TYM, SO4
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 361 | 54% helix, 12% strand | O59584 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 363 | 55% helix, 12% strand | O59584 |
Ligands and binding sites
- TYM · Tryptophanyl-5'amp · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.76 | 0.86 | 51 | TYM, SO4 |
| 2 | 400 | 0.76 | 0.86 | 58 | TYM, SO4 |
| 3 | 191 | 0.61 | 0.82 | 35 | empty |
| 4 | 198 | 0.49 | 0.75 | 21 | empty |
| 5 | 191 | 0.47 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1954 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3JXE · Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O59584 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (O59584) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O59584
- Elsewhere: RCSB PDB 3JXE · PDBe 3JXE · UniProt O59584
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