MolNFT v1 · #166710 · protein
Crystal structure of prolyl-tRNA synthetase from naegleria fowleri in complex with halofuginone and amppnp
6UYH: “Crystal structure of prolyl-tRNA synthetase from naegleria fowleri in complex with halofuginone and amppnp”. X-ray diffraction, 4 ligands (ANP, HFG, MG), 13 pockets (best druggability 0.79). MolNFT v1 #166710 on GenesisL1: 3D…
- PDB
- 6UYH
- Type
- protein
- Length
- 986 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase
- Ligands
- ANP, HFG, MG, SO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase | protein | 493 | 37% helix, 28% strand | — |
| B | Prolyl-tRNA synthetase | protein | 493 | 37% helix, 28% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- HFG · 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.79 | 0.81 | 76 | empty |
| 2 | 666 | 0.76 | 0.82 | 56 | ANP, HFG, MG |
| 3 | 583 | 0.76 | 0.83 | 51 | ANP, HFG, MG |
| 4 | 120 | 0.57 | 0.84 | 25 | empty |
| 5 | 132 | 0.56 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2140 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6UYH · Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri 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
- Elsewhere: RCSB PDB 6UYH · PDBe 6UYH
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