Research workbench
Crystal structure of HPV6A E2 DNA binding domain bound to an 18 base pair DNA target
Analyse Crystal structure of HPV6A E2 DNA binding domain bound to an 18 base pair DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AYG
- Type
- protein + DNA
- Length
- 210 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*GP*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*GP*C)- 3'; Regulatory protein E2
- UniProt
- Q84294
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'- D(*GP*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*GP*C)- 3' | dna | 18 | — | — |
| A, B | Regulatory protein E2 | protein | 87 | 29% helix, 29% strand | Q84294 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.48 | 0.81 | 25 | empty |
| 2 | 55 | 0.41 | 0.82 | 16 | empty |
| 3 | 97 | 0.36 | 0.75 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1292 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 791 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- C–B · 395 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–B · 358 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–A · 358 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 2AYG · Crystal structure of HPV6a E2 DNA binding domain bound to an 18 base pair DNA target · the same entry in another collection · chain C against C, 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 2AYG · PDBe 2AYG · UniProt Q84294
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.