Research workbench
Structure of a HPRP31-15.5K-U4ATAC 5' stem loop complex, monomeric form
Analyse Structure of a HPRP31-15.5K-U4ATAC 5' stem loop complex, monomeric form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SIU
- Type
- protein + RNA
- Length
- 777 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NHP2-like protein 1; U4/U6 small nuclear ribonucleoprotein PRP31; U4ATAC snrna
- UniProt
- P55769, Q8WWY3
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | NHP2-like protein 1 | protein | 125 | 48% helix, 16% strand | P55769 |
| B | U4/U6 small nuclear ribonucleoprotein PRP31 | protein | 235 | 71% helix, 0% strand | Q8WWY3 |
| C, F | U4ATAC snrna | rna | 28 | — | — |
| E | U4/U6 small nuclear ribonucleoprotein PRP31 | protein | 236 | 73% helix, 0% strand | Q8WWY3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.65 | 0.81 | 47 | empty |
| 2 | 130 | 0.47 | 0.78 | 13 | empty |
| 3 | 76 | 0.38 | 0.78 | 18 | empty |
| 4 | 59 | 0.32 | 0.77 | 20 | empty |
| 5 | 78 | 0.31 | 0.73 | 22 | SO4 |
Interfaces
7 interfaces between chains.
- B–E · 1383 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 776 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 722 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–F · 653 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–C · 628 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 3SIU · Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, monomeric form · the same entry in another collection · chain F against F, TM-score 1.00
- P55769 · AlphaFold monomer V2.0 prediction for NHP2-like protein 1 (P55769) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q8WWY3 · AlphaFold monomer V2.0 prediction for U4/U6 small nuclear ribonucleoprotein PRP31 (Q8WWY3) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P55769
- Every structure of UniProt Q8WWY3
- Elsewhere: RCSB PDB 3SIU · PDBe 3SIU · UniProt P55769 · UniProt Q8WWY3
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