Research workbench
Crystal of plasmodium falciparum tyrosyl-tRNA synthetase (PFTYRRS)IN complex with adenylate analog
Analyse Crystal of plasmodium falciparum tyrosyl-tRNA synthetase (PFTYRRS)IN complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VGJ
- Type
- protein
- Length
- 709 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-tRNA synthetase, putative
- EC
- 6.1.1.1
- UniProt
- Q8IAR7
- Ligands
- TYR, AMP
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-tRNA synthetase, putative (EC 6.1.1.1) | protein | 353 | 57% helix, 11% strand | Q8IAR7 |
| B | Tyrosyl-tRNA synthetase, putative (EC 6.1.1.1) | protein | 356 | 54% helix, 11% strand | Q8IAR7 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.76 | 0.86 | 43 | TYR, AMP |
| 2 | 328 | 0.75 | 0.86 | 40 | TYR, AMP |
| 3 | 180 | 0.47 | 0.75 | 33 | empty |
| 4 | 107 | 0.42 | 0.77 | 25 | empty |
| 5 | 104 | 0.38 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1379 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3VGJ · Crystal of Plasmodium falciparum tyrosyl-tRNA synthetase (PfTyrRS)in complex with… · the same entry in another collection · chain B against B, 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 Q8IAR7
- Elsewhere: RCSB PDB 3VGJ · PDBe 3VGJ · UniProt Q8IAR7
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