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MolNFT v1 · #68509 · protein + DNA

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

3JY1: “Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing an abasic site (across from C)”. X-ray diffraction, 2 pockets (best druggability 0.75). MolNFT v1 #68509 on GenesisL1: 3D structure, binding sites and pockets…

PDB
3JY1
Type
protein + DNA
Length
246 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 0.75

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
AAlkylpurine DNA glycosylase alkdprotein22674% 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*CP*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
18130.750.7947empty
2540.310.7711empty

Interfaces

3 interfaces between chains.

  • A–C · 512 Ų buried · 12 hydrogen bonds · protein-nucleic
  • B–C · 440 Ų buried · 35 hydrogen bonds · nucleic-nucleic
  • A–B · 350 Ų buried · 10 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 3JY1 · 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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