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Alkylpurine DNA glycosylase alkd bound to DNA containing a 3- methyladenine analog (100% substrate at 4 hours)

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: 5CL3
Type: protein + DNA
Length: 255 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alkd; DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3'); DNA…
EC: 3.2.2.-
UniProt: R8GWR7
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 72% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alkd (EC 3.2.2.-)	protein	231	72% helix, 1% strand	R8GWR7
B	DNA (5'-D(CPCPCPGPAP(DZM)PAPGPTPCPCPG)-3')	dna	12	—	—
C	DNA (5'-D(CPGPGPAPCPTPTPTPCPGPGPG)-3')	dna	12	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	883	0.77	0.80	48	empty
2	323	0.57	0.77	26	empty

Interfaces

3 interfaces between chains.

B–C · 557 Å² buried · 56 hydrogen bonds · nucleic-nucleic
A–B · 520 Å² buried · 11 hydrogen bonds · protein-nucleic
A–C · 282 Å² buried · 6 hydrogen bonds · protein-nucleic

Modifications

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

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Every structure of UniProt R8GWR7
Elsewhere: RCSB PDB 5CL3 · PDBe 5CL3 · UniProt R8GWR7

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