MolNFT v1 · #168650 · protein
Tyrosyl T-RNA synthetase mutant from E.COLI complexed with sulfotyrosine
6WN2 · Tyrosine--tRNA ligase: “Tyrosyl T-RNA synthetase mutant from E.COLI complexed with sulfotyrosine”. X-ray diffraction, 3 ligands (TYS, NA, SO4), 6 pockets (best druggability 0.72). MolNFT v1 #168650 on GenesisL1: 3D structure…
- PDB
- 6WN2
- Type
- protein
- Length
- 636 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
- A0A3Q0MY83
- Ligands
- TYS, NA, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 318 | 56% helix, 13% strand | A0A3Q0MY83 |
Ligands and binding sites
- TYS · O-sulfo-L-tyrosine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 5 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.72 | 0.83 | 51 | TYS, SO4 |
| 2 | 437 | 0.72 | 0.82 | 51 | TYS, SO4 |
| 3 | 59 | 0.40 | 0.81 | 13 | empty |
| 4 | 93 | 0.38 | 0.77 | 19 | PG4 |
| 5 | 73 | 0.32 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1695 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6WN2 · Tyrosyl t-RNA Synthetase Mutant from E.coli Complexed with sulfotyrosine · 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 A0A3Q0MY83
- Elsewhere: RCSB PDB 6WN2 · PDBe 6WN2 · UniProt A0A3Q0MY83
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