MolNFT v1 · #49646 · protein
Crystal structures of human tryptophanyl-tRNA synthetase in complex with tryptophanamide and ATP
2QUI: “Crystal structures of human tryptophanyl-tRNA synthetase in complex with tryptophanamide and ATP”. X-ray diffraction, 3 ligands (LTN, ATP, MG), 6 pockets (best druggability 0.78). MolNFT v1 #49646 on GenesisL1: 3D structure, binding…
- PDB
- 2QUI
- Type
- protein
- Length
- 769 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
- P23381
- Ligands
- LTN, ATP, MG
- Pockets
- 6 · best druggability 0.78
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 | 390 | 54% helix, 13% strand | P23381 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 379 | 54% helix, 11% strand | P23381 |
Ligands and binding sites
- LTN · L-tryptophanamide · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.78 | 0.89 | 41 | LTN, MG, ATP |
| 2 | 617 | 0.72 | 0.79 | 60 | LTN |
| 3 | 255 | 0.56 | 0.77 | 29 | empty |
| 4 | 179 | 0.47 | 0.75 | 18 | empty |
| 5 | 122 | 0.42 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1552 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2QUI · Crystal structures of human tryptophanyl-tRNA synthetase in complex with Tryptophanamide… · the same entry in another collection · chain B against B, TM-score 1.00
- P23381 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase, cytoplasmic (P23381) · a predicted model of the same protein · chain A 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 P23381
- Elsewhere: RCSB PDB 2QUI · PDBe 2QUI · UniProt P23381
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