Research workbench
Crystal structure of tyrosine-tRNA synthetase from acinetobacter baumannii with bound L-tyrosine
Analyse Crystal structure of tyrosine-tRNA synthetase from acinetobacter baumannii with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BQZ
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine--tRNA ligase
- EC
- 6.1.1.1
- UniProt
- A0A086HYS2
- Ligands
- TYR, MG
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 215 | 52% helix, 14% strand | A0A086HYS2 |
| B | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 215 | 50% helix, 14% strand | A0A086HYS2 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.63 | 0.80 | 37 | TYR |
| 2 | 283 | 0.62 | 0.80 | 38 | TYR |
| 3 | 69 | 0.42 | 0.80 | 17 | empty |
| 4 | 54 | 0.37 | 0.79 | 16 | empty |
| 5 | 81 | 0.35 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 469 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6BQZ · Crystal Structure of Tyrosine-tRNA Synthetase from Acinetobacter baumannii with bound… · the same entry in another collection · chain A against A, 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 A0A086HYS2
- Elsewhere: RCSB PDB 6BQZ · PDBe 6BQZ · UniProt A0A086HYS2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.