MolNFT v1 · #102120 · DNA

In and out the minor groove: interaction of an at rich-DNA with the CD27 drug

4OCD · D(AAAATTTT): “In and out the minor groove: interaction of an at rich-DNA with the CD27 drug”. X-ray diffraction, 1 ligand (MWB). MolNFT v1 #102120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OCD
Type: DNA
Length: 24 nucleotides
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D(AAAATTTT)
Ligands: MWB

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	D(AAAATTTT)	dna	8	—	—

Ligands and binding sites

MWB · N1-(4,5-dihydro-1H-imidazol-2-yl)-N4-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzene-1,4-diamine · ligand · 3 copies · chains A, C, B

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

Interfaces

3 interfaces between chains.

B–C · 337 Å² buried · 29 hydrogen bonds · nucleic-nucleic
A–B · 143 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–C · 22 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

4OCD · In and Out the minor groove: Interaction of an AT rich-DNA with the CD27 drug · 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 4OCD · PDBe 4OCD

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