Research workbench
Crystal structure of the HPV16 E6/E6AP/P53 ternary complex at 2.25 a resolution
Analyse Crystal structure of the HPV16 E6/E6AP/P53 ternary complex at 2.25 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XR8
- Type
- protein
- Length
- 1,456 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein, ubiquitin ligase E6AP; Cellular tumor antigen P53…
- UniProt
- P0AEX9, P04637, P03126
- Ligands
- GLC, ZN
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein, ubiquitin ligase E6AP | protein | 383 | 44% helix, 20% strand | P0AEX9 |
| B | Maltose-binding periplasmic protein, ubiquitin ligase E6AP | protein | 381 | 43% helix, 20% strand | P0AEX9 |
| C, D | Cellular tumor antigen P53 | protein | 199 | 10% helix, 33% strand | P04637 |
| F | Protein E6 | protein | 143 | 36% helix, 19% strand | P03126 |
| H | Protein E6 | protein | 151 | 34% helix, 18% strand | P03126 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains C, D, F, H
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, H, B, D, F
- EDO · 1,2-ethanediol · additive · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.83 | 0.84 | 118 | empty |
| 2 | 783 | 0.79 | 0.83 | 88 | empty |
| 3 | 383 | 0.77 | 0.87 | 57 | empty |
| 4 | 243 | 0.73 | 0.87 | 29 | GLC |
| 5 | 409 | 0.73 | 0.83 | 48 | empty |
Interfaces
10 interfaces between chains.
- D–H · 1245 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1195 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1158 Ų buried · 20 hydrogen bonds · protein-protein
- B–H · 1113 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 415 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4XR8 · Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution · 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 P0AEX9
- Every structure of UniProt P04637
- Every structure of UniProt P03126
- Elsewhere: RCSB PDB 4XR8 · PDBe 4XR8 · UniProt P0AEX9 · UniProt P04637 · UniProt P03126
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