MolNFT v1 · #152050 · protein
Crystal structure of E. COLI tyrrs in complex with 5'-O-(N-L-tyrosyl) sulfamoyl-adenosine
6I5Y · Tyrosine--tRNA ligase: “Crystal structure of E. COLI tyrrs in complex with 5'-O-(N-L-tyrosyl) sulfamoyl-adenosine”. X-ray diffraction, 1 ligand (YSA), 5 pockets (best druggability 0.69). MolNFT v1 #152050 on GenesisL1: 3D structure…
- PDB
- 6I5Y
- Type
- protein
- Length
- 826 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
- A0A140NBN7
- Ligands
- YSA
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 411 | 52% helix, 14% strand | A0A140NBN7 |
| B | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 415 | 52% helix, 14% strand | A0A140NBN7 |
Ligands and binding sites
- YSA · 5'-O-[N-(L-tyrosyl)sulfamoyl]adenosine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.69 | 0.82 | 37 | YSA |
| 2 | 438 | 0.68 | 0.80 | 49 | YSA |
| 3 | 75 | 0.52 | 0.85 | 25 | empty |
| 4 | 73 | 0.34 | 0.76 | 13 | empty |
| 5 | 56 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1719 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6I5Y · Crystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyrosyl)sulfamoyl-adenosine · 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 A0A140NBN7
- Elsewhere: RCSB PDB 6I5Y · PDBe 6I5Y · UniProt A0A140NBN7
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