Research workbench
Open and closed forms of wild-type human PRP8 RNase H-like domain with bound co ion
Analyse Open and closed forms of wild-type human PRP8 RNase H-like domain with bound co… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JK9
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-processing-splicing factor 8
- UniProt
- Q6P2Q9
- Ligands
- CO, CL
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-processing-splicing factor 8 | protein | 219 | 43% helix, 20% strand | Q6P2Q9 |
| B | Pre-mRNA-processing-splicing factor 8 | protein | 220 | 40% helix, 16% strand | Q6P2Q9 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A, 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 | 571 | 0.69 | 0.78 | 51 | GOL |
| 2 | 78 | 0.62 | 0.89 | 21 | CO |
| 3 | 245 | 0.56 | 0.77 | 21 | empty |
| 4 | 95 | 0.46 | 0.80 | 21 | empty |
| 5 | 117 | 0.44 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 977 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4JK9 · Open and closed forms of wild-type human PRP8 RNase H-like domain with bound Co ion · the same entry in another collection · chain A against A, TM-score 1.00
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 4JK9 · PDBe 4JK9 · UniProt Q6P2Q9
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