MolNFT v1 · #80528 · protein
Crystal structure of tryptophanyl-tRNA synthetase from campylobacter jejuni complexed with ADP and tryptophane
3TZL: “Crystal structure of tryptophanyl-tRNA synthetase from campylobacter jejuni complexed with ADP and tryptophane”. X-ray diffraction, 4 ligands (ADP, TRP, NA), 6 pockets (best druggability 0.75). MolNFT v1 #80528 on GenesisL1: 3D…
- PDB
- 3TZL
- Type
- protein
- Length
- 639 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
- Q9PIB4
- Ligands
- ADP, TRP, NA, PO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 319 | 61% helix, 8% strand | Q9PIB4 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 320 | 58% helix, 9% strand | Q9PIB4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
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 | 833 | 0.75 | 0.79 | 62 | ADP, TRP, NA |
| 2 | 602 | 0.67 | 0.76 | 49 | ADP, TRP |
| 3 | 226 | 0.62 | 0.82 | 45 | empty |
| 4 | 98 | 0.45 | 0.79 | 18 | empty |
| 5 | 56 | 0.37 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1755 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3TZL · Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PIB4 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (Q9PIB4) · 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 Q9PIB4
- Elsewhere: RCSB PDB 3TZL · PDBe 3TZL · UniProt Q9PIB4
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