Research workbench
Crystal structure of seryl-tRNA synthetase from candida albicans
Analyse Crystal structure of seryl-tRNA synthetase from candida albicans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QO8
- Type
- protein
- Length
- 441 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seryl-tRNA synthetase, cytoplasmic
- EC
- 6.1.1.11
- UniProt
- Q9HGT6
- Ligands
- SSA, MG
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Seryl-tRNA synthetase, cytoplasmic (EC 6.1.1.11) | protein | 441 | 43% helix, 22% strand | Q9HGT6 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.72 | 0.80 | 60 | SSA, MG |
| 2 | 114 | 0.35 | 0.73 | 19 | empty |
| 3 | 69 | 0.34 | 0.76 | 15 | empty |
Compared structures
- 3QO8 · Crystal Structure of seryl-tRNA synthetase from Candida albicans · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HGT6 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase, cytoplasmic (Q9HGT6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9HGT6
- Elsewhere: RCSB PDB 3QO8 · PDBe 3QO8 · UniProt Q9HGT6
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