MolNFT v1 · #98686 · protein + RNA
Crystal structure of the catalytic domain of rlub in complex with a 21-nucleotide RNA substrate
4LGT · Ribosomal large subunit pseudouridine synthase B: “Crystal structure of the catalytic domain of rlub in complex with a 21-nucleotide RNA substrate”. X-ray diffraction, 8 pockets (best druggability 0.68). MolNFT v1 #98686 on…
- PDB
- 4LGT
- Type
- protein + RNA
- Length
- 539 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal large subunit pseudouridine synthase B; Stem-loop of 23S rRNA
- EC
- 5.4.99.22
- UniProt
- P37765
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal large subunit pseudouridine synthase B (EC 5.4.99.22) | protein | 251 | 22% helix, 30% strand | P37765 |
| E | Stem-loop of 23S rRNA | rna | 21 | — | — |
| D | Ribosomal large subunit pseudouridine synthase B (EC 5.4.99.22) | protein | 247 | 22% helix, 30% strand | P37765 |
| F | Stem-loop of 23S rRNA | rna | 20 | — | — |
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.68 | 0.97 | 24 | empty |
| 2 | 208 | 0.49 | 0.76 | 28 | empty |
| 3 | 94 | 0.48 | 0.81 | 25 | empty |
| 4 | 96 | 0.39 | 0.76 | 20 | empty |
| 5 | 150 | 0.38 | 0.73 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–E · 1841 Ų buried · 68 hydrogen bonds · protein-nucleic
- D–F · 1837 Ų buried · 71 hydrogen bonds · protein-nucleic
- A–D · 704 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 229 Ų buried · 2 hydrogen bonds · protein-nucleic
- E–D · 226 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification, oxidation).
Compared structures
- 4LGT · Crystal structure of the catalytic domain of RluB in complex with a 21-nucleotide RNA… · the same entry in another collection · chain A against A, TM-score 1.00
- P37765 · AlphaFold monomer V2.0 prediction for ribosomal large subunit pseudouridine synthase B… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P37765
- Elsewhere: RCSB PDB 4LGT · PDBe 4LGT · UniProt P37765
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