MolNFT v1 · #31125 · protein + RNA
Structure of human tryptophanyl-tRNA synthetase in complex with TRNA(TRP)
2AKE · Transfer RNA-TRP: “Structure of human tryptophanyl-tRNA synthetase in complex with TRNA(TRP)”. X-ray diffraction, 2 ligands (TRP, SO4), 6 pockets (best druggability 0.72). MolNFT v1 #31125 on GenesisL1: 3D structure, binding sites…
- PDB
- 2AKE
- Type
- protein + RNA
- Length
- 445 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transfer RNA-TRP; Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- P23381
- Ligands
- TRP, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Transfer RNA-TRP | rna | 72 | — | — |
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 373 | 55% helix, 11% strand | P23381 |
Ligands and binding sites
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 | 680 | 0.72 | 0.79 | 68 | SO4, TRP |
| 2 | 790 | 0.66 | 0.75 | 35 | empty |
| 3 | 546 | 0.62 | 0.75 | 34 | empty |
| 4 | 204 | 0.54 | 0.78 | 25 | empty |
| 5 | 93 | 0.39 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 576 Ų buried · 27 hydrogen bonds · protein-nucleic
Compared structures
- 2AKE · Structure of human tryptophanyl-tRNA synthetase in complex with tRNA(Trp) · 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 2AKE · PDBe 2AKE · UniProt P23381
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