Research workbench
Open and closed forms of T1791P+R1865A human PRP8 RNase H-like domain with bound Mg ion
Analyse Open and closed forms of T1791P+R1865A human PRP8 RNase H-like domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JKF
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Homo sapiens
- Molecule
- Pre-mRNA-processing-splicing factor 8
- UniProt
- Q6P2Q9
- Ligands
- MG
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.95 · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-processing-splicing factor 8 | protein | 220 | 43% helix, 16% strand | Q6P2Q9 |
| B | Pre-mRNA-processing-splicing factor 8 | protein | 210 | 42% helix, 17% strand | Q6P2Q9 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.64 | 0.88 | 29 | empty |
| 2 | 401 | 0.63 | 0.77 | 30 | empty |
| 3 | 255 | 0.55 | 0.76 | 25 | empty |
| 4 | 112 | 0.46 | 0.79 | 25 | empty |
| 5 | 111 | 0.43 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1001 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4JKF · Open and closed forms of T1791P+R1865A human PRP8 RNase H-like domain with bound mg ion · the same entry in another collection · chain A against A, TM-score 1.00
- Q6P2Q9 · AlphaFold monomer V2.0 prediction for pre-mRNA-processing-splicing factor 8 (Q6P2Q9) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q6P2Q9
- Elsewhere: RCSB PDB 4JKF · PDBe 4JKF · UniProt Q6P2Q9
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