Research workbench
Open and closed forms of I1790Y human PRP8 RNase H-like domain with bound mg ion
Analyse Open and closed forms of I1790Y 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
- 4JKD
- Type
- protein
- Length
- 440 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
- 7 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pre-mRNA-processing-splicing factor 8 | protein | 220 | 43% helix, 20% strand | Q6P2Q9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.67 | 0.78 | 46 | CL |
| 2 | 119 | 0.64 | 0.88 | 31 | MG |
| 3 | 206 | 0.51 | 0.76 | 20 | empty |
| 4 | 111 | 0.48 | 0.80 | 21 | empty |
| 5 | 94 | 0.41 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1004 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4JKD · Open and closed forms of I1790Y 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 4JKD · PDBe 4JKD · UniProt Q6P2Q9
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