Research workbench
Crystal structure of the catalytic domain of E. COLI pseudouridine synthase rluc
Analyse Crystal structure of the catalytic domain of E. COLI 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
- 1XPI
- Type
- protein
- Length
- 458 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
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70) | protein | 229 | 22% helix, 32% strand | P0AA39 |
| B | Ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70) | protein | 229 | 23% helix, 33% strand | P0AA39 |
Ligands and binding sites
- ACY · Acetic acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.81 | 0.84 | 80 | ACY |
| 2 | 243 | 0.66 | 0.83 | 30 | empty |
| 3 | 189 | 0.54 | 0.79 | 34 | empty |
| 4 | 118 | 0.42 | 0.76 | 25 | empty |
| 5 | 78 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1246 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1XPI · Crystal structure of the catalytic domain of E. coli pseudouridine synthase RluC · 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 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 P0AA39
- Elsewhere: RCSB PDB 1XPI · PDBe 1XPI · UniProt P0AA39
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