MolNFT v1 · #124712 · protein + DNA

Muty N-terminal domain in complex with undamaged DNA

5KN8 · Adenine DNA glycosylase: “Muty N-terminal domain in complex with undamaged DNA”. X-ray diffraction, 2 ligands (SF4, CA), 3 pockets (best druggability 0.69). MolNFT v1 #124712 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5KN8
Type: protein + DNA
Length: 242 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenine DNA glycosylase; DNA (5'-D(*AP*TP*CP*CP*TP*GP*TP*GP*CP*T)-3'); DNA…
EC: 3.2.2.-
UniProt: P83847
Ligands: SF4, CA
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenine DNA glycosylase (EC 3.2.2.-)	protein	222	65% helix, 0% strand	P83847
C	DNA (5'-D(APTPCPCPTPGPTPGPCPT)-3')	dna	10	—	—
D	DNA (5'-D(APGPCPAPCPAPGPGPAPT)-3')	dna	10	—	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains A
CA · Calcium ion · metal · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	553	0.69	0.79	54	empty
2	218	0.62	0.82	22	empty
3	199	0.53	0.78	29	CA

Interfaces

3 interfaces between chains.

C–D · 503 Å² buried · 51 hydrogen bonds · nucleic-nucleic
A–D · 502 Å² buried · 15 hydrogen bonds · protein-nucleic
A–C · 328 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

5KN8 · MutY N-terminal domain in complex with undamaged DNA · the same entry in another collection · chain A against A, TM-score 1.00
P83847 · AlphaFold monomer V2.0 prediction for adenine DNA glycosylase (P83847) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P83847
Elsewhere: RCSB PDB 5KN8 · PDBe 5KN8 · UniProt P83847

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