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A new form of DNA-drug interaction in the minor groove of a coiled coil

Analyse A new form of DNA-drug interaction in the minor groove of a coiled coil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EY0
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DT)-3'
Ligands: PNT, MG
Pockets: 1 · best druggability 0.24

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(DAPDTPDAPDTPDAPDTPDAPDTPDAPDT)-3'	dna	10	—	—

Ligands and binding sites

PNT · 1,5-bis(4-amidinophenoxy)pentane · 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	52	0.24	0.73	12	PNT

Interfaces

1 interface between chains.

A–B · 433 Å² buried · 36 hydrogen bonds · nucleic-nucleic

Compared structures

3EY0 · A new form of DNA-drug interaction in the minor groove of a coiled coil · 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 3EY0 · PDBe 3EY0

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