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Huaa 19BP sym DNA pH 5.5

Analyse Huaa 19BP sym DNA pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6O6K
Type
protein + DNA
Length
166 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA-binding protein hu-alpha; DNA (5'-D(P*AP*TP*TP*TP*CP*AP*TP*GP*AP*T)-3'); DNA…
UniProt
P0ACF2
Pockets
2 · best druggability 0.45

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 21% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA-binding protein hu-alphaprotein7748% helix, 19% strandP0ACF2
BDNA-binding protein hu-alphaprotein6954% helix, 22% strandP0ACF2
CDNA (5'-D(P*AP*TP*TP*TP*CP*AP*TP*GP*AP*T)-3')dna10——
DDNA (5'-D(P*CP*AP*TP*CP*AP*TP*GP*AP*AP*A)-3')dna10——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11200.450.7916empty
21150.370.7417empty

Interfaces

5 interfaces between chains.

  • A–B · 1859 Ų buried · 13 hydrogen bonds · protein-protein
  • C–D · 399 Ų buried · 23 hydrogen bonds · nucleic-nucleic
  • B–C · 212 Ų buried · 3 hydrogen bonds · protein-nucleic
  • A–D · 168 Ų buried · 3 hydrogen bonds · protein-nucleic
  • B–D · 58 Ų buried · 0 hydrogen bonds · protein-nucleic

Compared structures

  • 6O6K · HUaa 19bp SYM DNA pH 5.5 · the same entry in another collection · chain A against A, TM-score 1.00
  • P0ACF2 · AlphaFold monomer V2.0 prediction for DNA-binding protein hu-alpha (P0ACF2) · a predicted model of the same protein · chain B against A, TM-score 0.98

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