MolNFT v1 · #24895 · protein
The crystal structure of the catalytic domain of pseudouridine synthase rluc from escherichia COLI
1V9K · Ribosomal large subunit pseudouridine synthase C: “The crystal structure of the catalytic domain of pseudouridine synthase rluc from escherichia COLI”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.79). MolNFT v1…
- 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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