Research workbench
Prolyl-tRNA synthetase from enterococcus faecalis complexed with ATP, manganese and prolinol
Analyse Prolyl-tRNA synthetase from enterococcus faecalis complexed with ATP, manganese… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J3M
- Type
- protein
- Length
- 1,112 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase
- EC
- 6.1.1.15
- UniProt
- Q831W7
- Ligands
- ATP, PRI, MN
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase (EC 6.1.1.15) | protein | 554 | 31% helix, 31% strand | Q831W7 |
| B | Prolyl-tRNA synthetase (EC 6.1.1.15) | protein | 558 | 31% helix, 31% strand | Q831W7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- PRI · Pyrrolidine-2-carbaldehyde · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.79 | 0.96 | 39 | empty |
| 2 | 823 | 0.74 | 0.78 | 54 | ATP, PRI, MN |
| 3 | 815 | 0.72 | 0.77 | 57 | ATP, PRI, MN |
| 4 | 502 | 0.65 | 0.77 | 49 | empty |
| 5 | 131 | 0.47 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2557 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2J3M · PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, manganese and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q831W7 · AlphaFold monomer V2.0 prediction for proline--tRNA ligase (Q831W7) · 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 Q831W7
- Elsewhere: RCSB PDB 2J3M · PDBe 2J3M · UniProt Q831W7
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