Research workbench
Trypanosoma brucei seryl-tRNA synthetase in complex with 5'-O-(N-(L- seryl)-SULFAMOYL)N3-methyluridine
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
- 6RLV
- Type
- protein
- Length
- 910 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
- FZT, NA
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Seryl-tRNA synthetase, putative (EC 6.1.1.11) | protein | 454 | 44% helix, 20% strand | D0A7P1 |
| B | Seryl-tRNA synthetase, putative (EC 6.1.1.11) | protein | 456 | 44% helix, 20% strand | D0A7P1 |
Ligands and binding sites
- FZT · 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine · 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 · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.80 | 0.99 | 22 | empty |
| 2 | 572 | 0.70 | 0.79 | 46 | NA, FZT |
| 3 | 523 | 0.69 | 0.79 | 54 | NA, FZT |
| 4 | 263 | 0.59 | 0.78 | 31 | GOL |
| 5 | 256 | 0.57 | 0.78 | 31 | GOL |
Interfaces
1 interface between chains.
- A–B · 2390 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6RLV · 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 6RLV · PDBe 6RLV · UniProt D0A7P1
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