Research workbench
Crystal structure of prolyl-tRNA synthetase from pseudomonas aeruginosa
Analyse Crystal structure of prolyl-tRNA synthetase from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UCM
- Type
- protein
- Length
- 1,129 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
- Q9I502
- Ligands
- MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 564 | 30% helix, 30% strand | Q9I502 |
| B | Proline--tRNA ligase (EC 6.1.1.15) | protein | 565 | 30% helix, 29% strand | Q9I502 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.76 | 0.82 | 82 | empty |
| 2 | 566 | 0.69 | 0.79 | 48 | MG |
| 3 | 611 | 0.69 | 0.78 | 50 | empty |
| 4 | 60 | 0.60 | 0.90 | 20 | empty |
| 5 | 115 | 0.49 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2661 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5UCM · Crystal Structure of Prolyl-tRNA Synthetase from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I502 · AlphaFold monomer V2.0 prediction for proline--tRNA ligase (Q9I502) · a predicted model of the same protein · chain B 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 Q9I502
- Elsewhere: RCSB PDB 5UCM · PDBe 5UCM · UniProt Q9I502
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