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Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing an abasic site (across from T)

Analyse Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3JXZ
Type
protein + DNA
Length
245 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Alkylpurine DNA glycosylase alkd; DNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3'); DNA…
UniProt
Q816E8
Pockets
2 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 74% helix, 1% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AAlkylpurine DNA glycosylase alkdprotein22574% helix, 1% strandQ816E8
BDNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3')dna10——
CDNA (5'-D(*AP*AP*AP*GP*CP*CP*TP*CP*CP*C)-3')dna10——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
17860.740.7946empty
2550.340.7912empty

Interfaces

3 interfaces between chains.

  • A–C · 516 Ų buried · 8 hydrogen bonds · protein-nucleic
  • B–C · 448 Ų buried · 31 hydrogen bonds · nucleic-nucleic
  • A–B · 343 Ų buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

  • 3JXZ · Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing an Abasic Site… · the same entry in another collection · chain A against A, TM-score 1.00

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