MolNFT v1 · #178244 · protein
Homo sapiens prolyl-tRNA synthetase (hsprs) in complex with L-proline and compound L96
7F99 · Bifunctional GLUTAMATE/PROLINE--tRNA ligase: “Homo sapiens prolyl-tRNA synthetase (hsprs) in complex with L-proline and compound L96”. X-ray diffraction, 5 ligands (1UI, PRO, CA), 12 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 7F99
- Type
- protein
- Length
- 972 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
- 1UI, PRO, CA, ZN, CL
- Pockets
- 12 · best druggability 0.76
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 | 484 | 37% helix, 29% strand | P07814 |
| B | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15) | protein | 488 | 38% helix, 29% strand | P07814 |
Ligands and binding sites
- 1UI · 4-[(3S)-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(5-methoxypyridin-3-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide · ligand · 2 copies · chains A, B
- PRO · Proline · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.76 | 0.84 | 48 | 1UI, CA, PRO |
| 2 | 463 | 0.75 | 0.84 | 48 | 1UI, PRO |
| 3 | 756 | 0.74 | 0.79 | 67 | empty |
| 4 | 362 | 0.61 | 0.77 | 29 | empty |
| 5 | 91 | 0.41 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2521 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 7F99 · Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96 · 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 0.99
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 7F99 · PDBe 7F99 · UniProt P07814
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