Research workbench
Crystal structure of human prolyl-tRNA synthetase in complex with halofuginone and ATP analogue
Analyse Crystal structure of human prolyl-tRNA synthetase in complex with halofuginone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HVC
- Type
- protein
- Length
- 965 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional GLUTAMATE/PROLINE--tRNA ligase
- EC
- 6.1.1.17, 6.1.1.15
- UniProt
- P07814
- Ligands
- ANP, HFG, MG, ZN
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15) | protein | 482 | 37% helix, 29% strand | P07814 |
| B | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15) | protein | 483 | 38% helix, 29% strand | P07814 |
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
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.79 | 0.84 | 61 | ANP, HFG, MG |
| 2 | 609 | 0.78 | 0.84 | 57 | ANP, HFG, MG |
| 3 | 827 | 0.75 | 0.79 | 70 | empty |
| 4 | 697 | 0.70 | 0.77 | 53 | empty |
| 5 | 139 | 0.49 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2448 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4HVC · Crystal structure of human prolyl-tRNA synthetase in complex with halofugi and ATP… · 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 B against A, TM-score 0.99
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 4HVC · PDBe 4HVC · UniProt P07814
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