MolNFT v1 · #115485 · protein + DNA

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

5CLB: “Alkylpurine DNA glycosylase alkd bound to DNA containing a 3- methyladenine analog (9-mer a)”. X-ray diffraction, 2 pockets (best druggability 0.79). MolNFT v1 #115485 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alkd (EC 3.2.2.-)	protein	224	73% helix, 1% strand	R8GWR7
B	DNA (5'-D(APAPGPCPAP(DZM)PAPCP*C)-3')	dna	9	—	—
C	DNA (5'-D(TPGPGPTPTPTPGPCP*T)-3')	dna	9	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	672	0.79	0.84	53	empty
2	133	0.44	0.76	16	empty

Interfaces

3 interfaces between chains.

A–B · 497 Å² buried · 12 hydrogen bonds · protein-nucleic
B–C · 396 Å² buried · 36 hydrogen bonds · nucleic-nucleic
A–C · 257 Å² buried · 8 hydrogen bonds · protein-nucleic

Modifications

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

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt R8GWR7
Elsewhere: RCSB PDB 5CLB · PDBe 5CLB · UniProt R8GWR7

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