MolNFT v1 · #27629 · protein
Crystal structure of the catalytic domain of E. COLI pseudouridine synthase rluc
1XPI · Ribosomal large subunit pseudouridine synthase C: “Crystal structure of the catalytic domain of E. COLI pseudouridine synthase rluc”. X-ray diffraction, 7 pockets (best druggability 0.81). MolNFT v1 #27629 on GenesisL1: 3D…
- 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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