MolNFT v1 · #31591 · protein + RNA
Charged and uncharged trnas adopt distinct conformations when complexed with human tryptophanyl-tRNA synthetase
2AZX · 72-mer: “Charged and uncharged trnas adopt distinct conformations when complexed with human tryptophanyl-tRNA…”. X-ray diffraction, 3 ligands (TRP, MG, SO4), 15 pockets (best druggability 0.76). MolNFT v1 #31591 on GenesisL1: 3D…
- PDB
- 2AZX
- Type
- protein + RNA
- Length
- 919 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 72-mer; Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- P23381
- Ligands
- TRP, MG, SO4
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 72-mer | rna | 72 | — | — |
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 387 | 52% helix, 13% strand | P23381 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 388 | 53% helix, 13% strand | P23381 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.76 | 0.85 | 47 | SO4, TRP |
| 2 | 457 | 0.76 | 0.85 | 47 | SO4, TRP |
| 3 | 687 | 0.67 | 0.77 | 28 | empty |
| 4 | 580 | 0.64 | 0.76 | 35 | empty |
| 5 | 570 | 0.62 | 0.76 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 764 Ų buried · 14 hydrogen bonds · protein-protein
- C–A · 697 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–B · 507 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 2AZX · Charged and uncharged tRNAs adopt distinct conformations when complexed with human… · 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 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 2AZX · PDBe 2AZX · UniProt P23381
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