MolNFT v1 · #157061 · protein
Crystal structure of prolyl-tRNA synthetase from onchocerca volvulus with bound halofuginone and nucleotide
6MN8 · Uncharacterized protein: “Crystal structure of prolyl-tRNA synthetase from onchocerca volvulus with bound halofuginone and nucleotide”. X-ray diffraction, 7 ligands (GLY, SER, HFG), 4 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 6MN8
- Type
- protein
- Length
- 399 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A0A2K6VKP7
- Ligands
- GLY, SER, HFG, ANP, AMP, 2PN, MG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 399 | 39% helix, 29% strand | A0A2K6VKP7 |
Ligands and binding sites
- GLY · Glycine · ligand · 3 copies · chains A
- SER · Serine · ligand · 2 copies · chains A
- HFG · 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains A
- 2PN · Imidodiphosphoric acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.69 | 0.81 | 42 | MG, HFG, ANP, AMP |
| 2 | 103 | 0.43 | 0.78 | 17 | empty |
| 3 | 87 | 0.34 | 0.74 | 17 | empty |
| 4 | 53 | 0.33 | 0.78 | 13 | empty |
Compared structures
- 6MN8 · Crystal Structure of Prolyl-tRNA Synthetase from Onchocerca volvulus with bound Halofugi… · 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 A0A2K6VKP7
- Elsewhere: RCSB PDB 6MN8 · PDBe 6MN8 · UniProt A0A2K6VKP7
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