Research workbench
The crystal structure of the catalytic domain of pseudouridine synthase rluc from escherichia COLI
Analyse The crystal structure of the catalytic domain of pseudouridine synthase rluc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V9K
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal large subunit pseudouridine synthase C
- EC
- 4.2.1.70
- UniProt
- P0AA39
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70) | protein | 227 | 22% helix, 32% strand | P0AA39 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.79 | 0.85 | 60 | empty |
| 2 | 170 | 0.66 | 0.86 | 31 | empty |
| 3 | 131 | 0.61 | 0.85 | 19 | empty |
| 4 | 136 | 0.45 | 0.77 | 24 | empty |
| 5 | 157 | 0.42 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1213 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 1V9K · The crystal structure of the catalytic domain of pseudouridine synthase RluC from… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AA39 · AlphaFold monomer V2.0 prediction for ribosomal large subunit pseudouridine synthase C… · 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 P0AA39
- Elsewhere: RCSB PDB 1V9K · PDBe 1V9K · UniProt P0AA39
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