Research workbench
Trypanosoma brucei seryl-tRNA synthetase in complex with 5'-O-(N-(L- seryl)-SULFAMOYL)URIDINE
Analyse Trypanosoma brucei seryl-tRNA synthetase in complex with 5'-O-(N-(L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RLT
- Type
- protein
- Length
- 912 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seryl-tRNA synthetase, putative
- EC
- 6.1.1.11
- UniProt
- D0A7P1
- Ligands
- FZK, NA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Seryl-tRNA synthetase, putative (EC 6.1.1.11) | protein | 456 | 45% helix, 20% strand | D0A7P1 |
Ligands and binding sites
- FZK · 5'-O-(N-(L-seryl)-Sulfamoyl)uridine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 6 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- MLI · Malonate ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.81 | 0.99 | 23 | empty |
| 2 | 605 | 0.71 | 0.79 | 56 | NA, FZK |
| 3 | 541 | 0.70 | 0.80 | 53 | NA, FZK |
| 4 | 274 | 0.59 | 0.78 | 29 | GOL |
| 5 | 250 | 0.56 | 0.78 | 29 | GOL |
Interfaces
1 interface between chains.
- A–B · 2371 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6RLT · Trypanosoma brucei Seryl-tRNA Synthetase in Complex with… · 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 D0A7P1
- Elsewhere: RCSB PDB 6RLT · PDBe 6RLT · UniProt D0A7P1
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