Research workbench
Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog
Analyse Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PID
- Type
- protein
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-tRNA synthetase
- EC
- 6.1.1.1
- UniProt
- Q9Y2Z4
- Ligands
- YSA
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 317 | 59% helix, 11% strand | Q9Y2Z4 |
| B | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 324 | 57% helix, 11% strand | Q9Y2Z4 |
Ligands and binding sites
- YSA · 5'-O-[N-(L-tyrosyl)sulfamoyl]adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.68 | 0.83 | 42 | YSA |
| 2 | 328 | 0.66 | 0.81 | 41 | YSA |
| 3 | 101 | 0.47 | 0.80 | 21 | empty |
| 4 | 79 | 0.42 | 0.80 | 17 | empty |
| 5 | 91 | 0.36 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1433 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2PID · Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9Y2Z4 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase, mitochondrial (Q9Y2Z4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9Y2Z4
- Elsewhere: RCSB PDB 2PID · PDBe 2PID · UniProt Q9Y2Z4
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