Research workbench
The Prp8 intein-cisplatin complex
Analyse The Prp8 intein-cisplatin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MYL
- Type
- protein
- Length
- 420 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.06
- Source
- Cryptococcus gattii serotype B
- Molecule
- Pre-mRNA-processing-splicing factor 8
- UniProt
- A0A095EAP2
- Ligands
- PT
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · resolution 3.06 · 1 distinct chain · 9% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pre-mRNA-processing-splicing factor 8 | protein | 140 | 9% helix, 55% strand | A0A095EAP2 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.71 | 0.79 | 71 | empty |
| 2 | 147 | 0.45 | 0.77 | 18 | empty |
| 3 | 114 | 0.39 | 0.75 | 19 | empty |
| 4 | 107 | 0.38 | 0.75 | 21 | empty |
| 5 | 65 | 0.29 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 426 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 217 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 6MYL · The PRP8 intein-cisplatin complex · 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 A0A095EAP2
- Elsewhere: RCSB PDB 6MYL · PDBe 6MYL · UniProt A0A095EAP2
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