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Solution structure of the aa-mismatch DNA complexed with naphthyridine-azaquinolone

Analyse Solution structure of the aa-mismatch DNA complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1X26
Type: DNA
Length: 22 nucleotides
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*TP*AP*AP*CP*AP*GP*AP*AP*TP*G)-3'; 5'-D(*CP*AP*TP*TP*CP*AP*GP*TP*TP*AP*G)-3'
Ligands: NAZ
Pockets: 1 · best druggability 0.23

Structure

solution nmr · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(CPTPAPAPCPAPGPAPAPTP*G)-3'	dna	11	—	—
B	5'-D(CPAPTPTPCPAPGPTPTPAP*G)-3'	dna	11	—	—

Ligands and binding sites

NAZ · N~3~-{3-[(7-methyl-1,8-naphthyridin-2-yl)amino]-3-oxopropyl}-N~1~-[(7-oxo-7,8-dihydro-1,8-naphthyridin-2-yl)methyl]-bet A-alaninamide · ligand · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.23	0.73	6	NAZ

Interfaces

1 interface between chains.

A–B · 486 Å² buried · 48 hydrogen bonds · nucleic-nucleic

Compared structures

1X26 · Solution structure of the AA-mismatch DNA complexed with naphthyridine-azaquinolone · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1X26 · PDBe 1X26

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