Research workbench
Crystal structure of a bacterial prors with ligands
Analyse Crystal structure of a bacterial prors with ligands in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZNJ
- Type
- protein
- Length
- 563 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
- A0A227M497
- Ligands
- ANP, HFG, MG, PO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 563 | 29% helix, 31% strand | A0A227M497 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- HFG · 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 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 | 700 | 0.72 | 0.79 | 58 | ANP, HFG, MG, GOL |
| 2 | 86 | 0.40 | 0.78 | 20 | empty |
| 3 | 93 | 0.40 | 0.77 | 22 | empty |
Compared structures
- 5ZNJ · Crystal structure of a bacterial ProRS with ligands · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A227M497
- Elsewhere: RCSB PDB 5ZNJ · PDBe 5ZNJ · UniProt A0A227M497
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