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Alkylpurine DNA glycosylase alkd bound to DNA containing a 3- methyladenine analog (9-mer a)

Analyse Alkylpurine DNA glycosylase alkd bound to DNA containing a 3- methyladenine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5CLB
Type
protein + DNA
Length
242 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Alkd; DNA (5'-D(*AP*AP*GP*CP*AP*(DZM)P*AP*CP*C)-3'); DNA…
EC
3.2.2.-
UniProt
R8GWR7
Pockets
2 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 73% helix, 1% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AAlkd (EC 3.2.2.-)protein22473% helix, 1% strandR8GWR7
BDNA (5'-D(*AP*AP*GP*CP*AP*(DZM)P*AP*CP*C)-3')dna9——
CDNA (5'-D(*TP*GP*GP*TP*TP*TP*GP*CP*T)-3')dna9——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
16720.790.8453empty
21330.440.7616empty

Interfaces

3 interfaces between chains.

  • A–B · 497 Ų buried · 12 hydrogen bonds · protein-nucleic
  • B–C · 396 Ų buried · 36 hydrogen bonds · nucleic-nucleic
  • A–C · 257 Ų buried · 8 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 5CLB · Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (9-mer… · the same entry in another collection · chain A against A, TM-score 1.00

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