Research workbench
Structure of E6AP-E6 complex in Att1 state
Analyse Structure of E6AP-E6 complex in Att1 state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8JRN
- Type
- protein
- Length
- 1,660 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens; Human papillomavirus 16
- Molecule
- Protein E6; Ubiquitin-protein ligase E3A
- EC
- 2.3.2.26
- UniProt
- P03126, Q05086
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · resolution 2.6 · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Protein E6 | protein | 141 | 39% helix, 17% strand | P03126 |
| C, A | Ubiquitin-protein ligase E3A (EC 2.3.2.26) | protein | 689 | 55% helix, 8% strand | Q05086 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.79 | 0.87 | 76 | empty |
| 2 | 614 | 0.77 | 0.83 | 80 | empty |
| 3 | 1164 | 0.74 | 0.77 | 106 | empty |
| 4 | 836 | 0.73 | 0.78 | 68 | empty |
| 5 | 480 | 0.71 | 0.81 | 56 | empty |
Interfaces
5 interfaces between chains.
- D–C · 1646 Ų buried · 26 hydrogen bonds · protein-protein
- B–A · 1642 Ų buried · 26 hydrogen bonds · protein-protein
- C–B · 517 Ų buried · 6 hydrogen bonds · protein-protein
- D–A · 517 Ų buried · 6 hydrogen bonds · protein-protein
- C–A · 230 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- Q05086 · AlphaFold monomer V2.0 prediction for ubiquitin-protein ligase E3A (Q05086) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P03126
- Every structure of UniProt Q05086
- Elsewhere: RCSB PDB 8JRN · PDBe 8JRN · UniProt P03126 · UniProt Q05086
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