MolNFT v1 · #139534 · protein
Crystal structure of eimeria tenella prolyl-tRNA synthetase (etprs) in complex with halofuginone
5XIP · Prolyl-tRNA synthetase, putative: “Crystal structure of eimeria tenella prolyl-tRNA synthetase (etprs) in complex with halofuginone”. X-ray diffraction, 3 ligands (ANP, HFG, MG), 20 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5XIP
- Type
- protein
- Length
- 1,866 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase, putative
- UniProt
- U6KWI1
- Ligands
- ANP, HFG, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase, putative | protein | 471 | 36% helix, 29% strand | U6KWI1 |
| B | Prolyl-tRNA synthetase, putative | protein | 475 | 36% helix, 28% strand | U6KWI1 |
| C | Prolyl-tRNA synthetase, putative | protein | 463 | 36% helix, 27% strand | U6KWI1 |
| D | Prolyl-tRNA synthetase, putative | protein | 457 | 36% helix, 28% strand | U6KWI1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- HFG · 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.77 | 0.86 | 37 | empty |
| 2 | 413 | 0.75 | 0.85 | 38 | empty |
| 3 | 703 | 0.74 | 0.80 | 57 | ANP, MG, HFG |
| 4 | 649 | 0.74 | 0.80 | 54 | ANP, MG, HFG |
| 5 | 50 | 0.71 | 0.99 | 15 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2563 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2555 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 5XIP · Crystal Structure of Eimeria tenella Prolyl-tRNA Synthetase (EtPRS) 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 U6KWI1
- Elsewhere: RCSB PDB 5XIP · PDBe 5XIP · UniProt U6KWI1
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