Research workbench
Crystal structure of prolyl-tRNA synthetase (prors, proline--tRNA ligase) from plasmodium falciparum 3D7
Analyse Crystal structure of prolyl-tRNA synthetase (prors, proline--tRNA ligase) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NCX
- Type
- protein
- Length
- 882 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline--tRNA ligase
- EC
- 6.1.1.15
- UniProt
- Q8I5R7
- Ligands
- CL
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 449 | 37% helix, 29% strand | Q8I5R7 |
| B | Proline--tRNA ligase (EC 6.1.1.15) | protein | 433 | 39% helix, 27% strand | Q8I5R7 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.73 | 0.81 | 42 | EDO |
| 2 | 469 | 0.72 | 0.81 | 44 | EDO |
| 3 | 175 | 0.65 | 0.85 | 28 | empty |
| 4 | 371 | 0.61 | 0.77 | 36 | EDO |
| 5 | 165 | 0.54 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1842 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4NCX · Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8I5R7 · AlphaFold monomer V2.0 prediction for proline--tRNA ligase (Q8I5R7) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q8I5R7
- Elsewhere: RCSB PDB 4NCX · PDBe 4NCX · UniProt Q8I5R7
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