Research workbench
Open and closed forms of V1788D human PRP8 RNase H-like domain with bound mg ion
Analyse Open and closed forms of V1788D human PRP8 RNase H-like domain with bound mg ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JKB
- Type
- protein
- Length
- 441 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
- MG, CL
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-processing-splicing factor 8 | protein | 221 | 43% helix, 20% strand | Q6P2Q9 |
| B | Pre-mRNA-processing-splicing factor 8 | protein | 220 | 39% helix, 16% strand | Q6P2Q9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, A
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.65 | 0.78 | 33 | GOL |
| 2 | 136 | 0.64 | 0.86 | 30 | GOL, MG |
| 3 | 238 | 0.53 | 0.76 | 22 | empty |
| 4 | 141 | 0.45 | 0.76 | 18 | empty |
| 5 | 70 | 0.45 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4JKB · Open and closed forms of V1788D human PRP8 RNase H-like domain with bound Mg 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 4JKB · PDBe 4JKB · UniProt Q6P2Q9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.