Research workbench
Structure of tyrosyl-tRNA synthetase refined at 2.3 ångströms resolution. interaction of the enzyme with the tyrosyl adenylate intermediate
Analyse Structure of tyrosyl-tRNA synthetase refined at 2.3 ångströms resolution.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TYD
- Type
- protein
- Length
- 317 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-tRNA synthetase
- EC
- 6.1.1.1
- UniProt
- P00952
- Ligands
- TYR
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 317 | 55% helix, 10% strand | P00952 |
Ligands and binding sites
- TYR · Tyrosine · ligand · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.70 | 0.81 | 50 | TYR |
| 2 | 145 | 0.43 | 0.74 | 23 | empty |
| 3 | 58 | 0.36 | 0.78 | 17 | empty |
Compared structures
- 1TYD · Structure of tyrosyl-tRNA synthetase refined at 2.3 ångströms resolution. interaction of… · the same entry in another collection · chain E against E, TM-score 1.00
- P00952 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase (P00952) · a predicted model of the same protein · chain E 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 P00952
- Elsewhere: RCSB PDB 1TYD · PDBe 1TYD · UniProt P00952
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