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Complex structure of DNA with self-catalyzed depurination activity

Analyse Complex structure of DNA with self-catalyzed depurination activity in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CPW
Type: protein + DNA
Length: 390 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase beta-like protein; DNA (5'- D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP…
UniProt: A0A0A1E3N6
Pockets: 2 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA polymerase beta-like protein	protein	175	31% helix, 31% strand	A0A0A1E3N6
a, b	DNA (5'- D(CPGPTPGPAPTPCPGPGPAPGPAPCPGPAPTPCPAPCPG)-3')	dna	20	—	—

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	400	0.61	0.76	53	empty
2	229	0.55	0.78	31	empty

Interfaces

3 interfaces between chains.

A–a · 584 Å² buried · 14 hydrogen bonds · protein-nucleic
B–b · 580 Å² buried · 14 hydrogen bonds · protein-nucleic
A–B · 184 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7CPW · Complex structure of DNA with self-catalyzed depurination activity · 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 A0A0A1E3N6
Elsewhere: RCSB PDB 7CPW · PDBe 7CPW · UniProt A0A0A1E3N6

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