MolNFT v1 · #97251 · protein
Crystal structure of human prolyl-tRNA synthetase (halofuginone bound form)
4K88 · Proline--tRNA ligase: “Crystal structure of human prolyl-tRNA synthetase (halofuginone bound form)”. X-ray diffraction, 2 ligands (HFG, ZN), 3 pockets (best druggability 0.77). MolNFT v1 #97251 on GenesisL1: 3D structure, binding…
- PDB
- 4K88
- Type
- protein
- Length
- 490 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline--tRNA ligase
- EC
- 6.1.1.15
- UniProt
- P07814
- Ligands
- HFG, ZN
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 490 | 36% helix, 27% strand | P07814 |
Ligands and binding sites
- HFG · 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.77 | 0.81 | 57 | HFG |
| 2 | 83 | 0.37 | 0.76 | 19 | empty |
| 3 | 55 | 0.27 | 0.73 | 16 | empty |
Compared structures
- 4K88 · Crystal structure of human prolyl-tRNA synthetase (halofugi bound form) · the same entry in another collection · chain A against A, TM-score 1.00
- P07814 · AlphaFold monomer V2.0 prediction for bifunctional GLUTAMATE/PROLINE --tRNA ligase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P07814
- Elsewhere: RCSB PDB 4K88 · PDBe 4K88 · UniProt P07814
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