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MolNFT v1 · #31543 · protein + DNA

Crystal structure of HPV6A E2 DNA binding domain bound to an 18 base pair DNA target

2AYG · 5'- D(*GP*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*GP*C)…: “Crystal structure of HPV6A E2 DNA binding domain bound to an 18 base pair DNA target”. X-ray diffraction, 3 pockets (best druggability 0.48). MolNFT v1 #31543 on…

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).

ChainMoleculeTypeResiduesSecondary structureUniProt
C, D5'- D(*GP*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*GP*C)- 3'dna18——
A, BRegulatory protein E2protein8729% helix, 29% strandQ84294

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11110.480.8125empty
2550.410.8216empty
3970.360.7528empty

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

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