MolNFT v1 · #33397 · protein
Crystal structure of methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate
2CJ9: “Crystal structure of methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate”. X-ray diffraction, 3 ligands (SSA, ZN, CL), 7 pockets (best druggability 0.75). MolNFT v1 #33397 on GenesisL1: 3D…
- PDB
- 2CJ9
- Type
- protein
- Length
- 970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seryl-tRNA synthetase
- EC
- 6.1.1.11
- UniProt
- Q46AN5
- Ligands
- SSA, ZN, CL
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 477 | 33% helix, 24% strand | Q46AN5 |
| B | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 493 | 35% helix, 25% strand | Q46AN5 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.75 | 0.80 | 88 | SSA |
| 2 | 639 | 0.72 | 0.79 | 67 | ZN, SSA |
| 3 | 421 | 0.63 | 0.77 | 39 | empty |
| 4 | 181 | 0.43 | 0.73 | 27 | empty |
| 5 | 69 | 0.36 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 5248 Ų buried · 73 hydrogen bonds · protein-protein
Compared structures
- 2CJ9 · Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with an… · the same entry in another collection · chain A against A, TM-score 1.00
- Q46AN5 · AlphaFold monomer V2.0 prediction for type-2 serine--tRNA ligase (Q46AN5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q46AN5
- Elsewhere: RCSB PDB 2CJ9 · PDBe 2CJ9 · UniProt Q46AN5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.