Research workbench
Crystal structure of seryl-tRNA synthetase from pyrococcus horikoshii complexed with a seryl-adenylate analog
Analyse Crystal structure of seryl-tRNA synthetase from pyrococcus horikoshii complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DQ0
- Type
- protein
- Length
- 894 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
- O58441
- Ligands
- SSA, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 447 | 44% helix, 22% strand | O58441 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 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 | 91 | 0.78 | 0.98 | 21 | empty |
| 2 | 767 | 0.75 | 0.80 | 63 | SO4, SSA |
| 3 | 748 | 0.74 | 0.79 | 61 | SO4, SSA |
| 4 | 81 | 0.34 | 0.75 | 17 | empty |
| 5 | 71 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2445 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 2DQ0 · Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with a… · the same entry in another collection · chain A against A, TM-score 1.00
- O58441 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase (O58441) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O58441
- Elsewhere: RCSB PDB 2DQ0 · PDBe 2DQ0 · UniProt O58441
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