MolNFT v1 · #68506 · protein + DNA

Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing a gt mismatch

3JXY: “Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing a gt mismatch”. X-ray diffraction, 2 pockets (best druggability 0.77). MolNFT v1 #68506 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3JXY
Type: protein + DNA
Length: 255 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alkylpurine DNA glycosylase alkd; DNA (5'-D(*CP*GP*GP*AP*CP*TP*GP*AP*CP*GP*GP*G)-3'); DNA…
UniProt: Q816E8
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 71% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alkylpurine DNA glycosylase alkd	protein	231	71% helix, 1% strand	Q816E8
B	DNA (5'-D(CPGPGPAPCPTPGPAPCPGPGPG)-3')	dna	12	—	—
C	DNA (5'-D(CPCPCPGPTPTPAPGPTPCPCPG)-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	894	0.77	0.80	53	empty
2	366	0.60	0.77	31	empty

Interfaces

3 interfaces between chains.

B–C · 555 Å² buried · 48 hydrogen bonds · nucleic-nucleic
A–C · 516 Å² buried · 13 hydrogen bonds · protein-nucleic
A–B · 290 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3JXY · Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing a GT Mismatch · the same entry in another collection · chain A against A, TM-score 1.00

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 Q816E8
Elsewhere: RCSB PDB 3JXY · PDBe 3JXY · UniProt Q816E8

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