Research workbench
Crystal structure of human H130R tryptophanyl-tRNA synthetase in complex with trpamp
Analyse Crystal structure of human H130R tryptophanyl-tRNA synthetase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UJJ
- Type
- protein
- Length
- 834 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan--tRNA ligase, cytoplasmic
- EC
- 6.1.1.2
- UniProt
- P23381
- Ligands
- TYM, MG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan--tRNA ligase, cytoplasmic (EC 6.1.1.2) | protein | 446 | 55% helix, 11% strand | P23381 |
| B | Tryptophan--tRNA ligase, cytoplasmic (EC 6.1.1.2) | protein | 388 | 53% helix, 14% strand | P23381 |
Ligands and binding sites
- TYM · Tryptophanyl-5'amp · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.81 | 0.90 | 44 | TYM, MG |
| 2 | 372 | 0.77 | 0.87 | 41 | TYM, MG |
| 3 | 289 | 0.59 | 0.78 | 35 | empty |
| 4 | 244 | 0.56 | 0.77 | 27 | empty |
| 5 | 280 | 0.52 | 0.75 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1588 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5UJJ · Crystal structure of human H130R tryptophanyl-tRNA synthetase in complex with TrpAMP · the same entry in another collection · chain A against A, TM-score 1.00
- P23381 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase, cytoplasmic (P23381) · a predicted model of the same protein · chain B 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 5UJJ · PDBe 5UJJ · UniProt P23381
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