MolNFT v1 · #142238 · protein
Structural basis for a tRNA synthetase
5ZY9 · Threonyl-tRNA synthase: “Structural basis for a tRNA synthetase”. X-ray diffraction, 2 ligands (2CR, ZN), 14 pockets (best druggability 0.80). MolNFT v1 #142238 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZY9
- Type
- protein
- Length
- 1,198 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonyl-tRNA synthase
- EC
- 6.1.1.3
- UniProt
- G3FIN0
- Ligands
- 2CR, ZN
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Threonyl-tRNA synthase (EC 6.1.1.3) | protein | 400 | 38% helix, 25% strand | G3FIN0 |
| E | Threonyl-tRNA synthase (EC 6.1.1.3) | protein | 398 | 38% helix, 25% strand | G3FIN0 |
Ligands and binding sites
- 2CR · (1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8, 16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid · ligand · 3 copies · chains C, D, E
- ZN · Zinc ion · metal · 3 copies · chains C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.80 | 0.81 | 79 | empty |
| 2 | 161 | 0.78 | 0.95 | 33 | empty |
| 3 | 575 | 0.69 | 0.78 | 48 | 2CR |
| 4 | 532 | 0.69 | 0.79 | 49 | 2CR |
| 5 | 494 | 0.68 | 0.79 | 42 | 2CR |
Interfaces
3 interfaces between chains.
- C–D · 2344 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1022 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 91 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZY9 · Structural basis for a tRNA synthetase · the same entry in another collection · chain C against C, TM-score 1.00
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 G3FIN0
- Elsewhere: RCSB PDB 5ZY9 · PDBe 5ZY9 · UniProt G3FIN0
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