Research workbench
Crystal structure of the unliganded E2 DNA binding domain from HPV6A
Analyse Crystal structure of the unliganded E2 DNA binding domain from HPV6A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AYE
- Type
- protein
- Length
- 520 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein E2
- UniProt
- Q84294
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Regulatory protein E2 | protein | 86 | 35% helix, 31% strand | Q84294 |
| B, C, D, E | Regulatory protein E2 | protein | 87 | 34% helix, 31% strand | Q84294 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 5 copies · chains B, A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.58 | 0.75 | 47 | empty |
| 2 | 167 | 0.48 | 0.77 | 23 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1390 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1307 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1292 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 415 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 262 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2AYE · Crystal structure of the unliganded E2 DNA Binding Domain from HPV6a · 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 Q84294
- Elsewhere: RCSB PDB 2AYE · PDBe 2AYE · UniProt Q84294
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