Research workbench
Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
Analyse Structure of a functional ribonucleoprotein pseudouridine synthase bound to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HJY
- Type
- protein + RNA
- Length
- 433 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudouridine synthase CBF5; Ribosome biogenesis protein NOP10…
- EC
- 5.4.99.-
- UniProt
- Q7LWY0, Q8U1R4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pseudouridine synthase CBF5 (EC 5.4.99.-) | protein | 320 | 27% helix, 32% strand | Q7LWY0 |
| B | Ribosome biogenesis protein NOP10 | protein | 53 | 23% helix, 17% strand | Q8U1R4 |
| C | 5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP *CP*GP*C)-3' | rna | 21 | — | — |
| D | RNA (25-mer) | rna | 25 | — | — |
| E | 5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3' | rna | 14 | — | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.74 | 0.78 | 50 | empty |
| 2 | 762 | 0.70 | 0.77 | 59 | empty |
| 3 | 157 | 0.46 | 0.76 | 21 | empty |
| 4 | 98 | 0.42 | 0.78 | 19 | empty |
| 5 | 108 | 0.34 | 0.73 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1428 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1058 Ų buried · 28 hydrogen bonds · protein-nucleic
- C–E · 662 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- C–D · 647 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- D–E · 388 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3HJY · Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate… · the same entry in another collection · chain B against B, TM-score 1.00
- Q7LWY0 · AlphaFold monomer V2.0 prediction for probable tRNA pseudouridine synthase B (Q7LWY0) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q8U1R4 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein NOP10 (Q8U1R4) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 Q7LWY0
- Every structure of UniProt Q8U1R4
- Elsewhere: RCSB PDB 3HJY · PDBe 3HJY · UniProt Q7LWY0 · UniProt Q8U1R4
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