Research workbench
Structure of HPV16 E6 oncoprotein in complex with IRF3 lxxll motif
Analyse Structure of HPV16 E6 oncoprotein in complex with IRF3 lxxll motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SJA
- Type
- protein
- Length
- 517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,INTERFERON regulatory factor 3; Protein…
- UniProt
- P0AEX9, Q14653, P03126
- Ligands
- GLC, ZN
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,INTERFERON regulatory factor 3 | protein | 383 | 46% helix, 20% strand | P0AEX9, Q14653 |
| B | Protein E6 | protein | 134 | 38% helix, 19% strand | P03126 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 5 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.72 | 0.83 | 31 | GLC |
| 2 | 318 | 0.60 | 0.78 | 35 | empty |
| 3 | 123 | 0.53 | 0.82 | 23 | empty |
| 4 | 70 | 0.40 | 0.79 | 16 | empty |
| 5 | 96 | 0.37 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1011 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6SJA · Structure of HPV16 E6 oncoprotein in complex with IRF3 LxxLL motif · the same entry in another collection · chain A against A, TM-score 1.00
- Q14653 · AlphaFold monomer V2.0 prediction for interferon regulatory factor 3 (Q14653) · a predicted model of the same protein · chain A against A, TM-score 0.26
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 P0AEX9
- Every structure of UniProt Q14653
- Every structure of UniProt P03126
- Elsewhere: RCSB PDB 6SJA · PDBe 6SJA · UniProt P0AEX9 · UniProt Q14653 · UniProt P03126
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