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Crystal structure analysis of the minor groove binding quinolinium quaternary salt sn 8224 complexed with cgcgaattcgcg

Analyse Crystal structure analysis of the minor groove binding quinolinium quaternary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZPI
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
Ligands: SN9, MG
Pockets: 1 · best druggability 0.29

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'	dna	12	—	—

Ligands and binding sites

SN9 · 8-methoxy-1-methyl-4-(4-(4-(1-methylpyridinium-4-ylamino)phenylcarbamoyl)phenylamino)quinolinium · ligand · chains A, B
MG · Magnesium ion · metal · 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	62	0.29	0.75	13	SN9

Interfaces

1 interface between chains.

A–B · 559 Å² buried · 53 hydrogen bonds · nucleic-nucleic

Compared structures

1ZPI · Crystal structure analysis of the minor groove binding quinolinium quaternary salt SN… · 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
Elsewhere: RCSB PDB 1ZPI · PDBe 1ZPI

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