MolNFT v1 · #29644 · DNA

Atc four-stranded DNA holliday junction

1ZF3 · 5'-D(*CP*CP*GP*AP*TP*AP*TP*CP*GP*G)-3': “Atc four-stranded DNA holliday junction”. X-ray diffraction, 1 ligand (CA), 1 pocket (best druggability 0.25). MolNFT v1 #29644 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZF3
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*CP*GP*AP*TP*AP*TP*CP*GP*G)-3'
Ligands: CA
Pockets: 1 · best druggability 0.25

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

CA · Calcium ion · metal · chains 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	61	0.25	0.72	8	empty

Interfaces

1 interface between chains.

A–B · 318 Å² buried · 34 hydrogen bonds · nucleic-nucleic

Compared structures

1ZF3 · ATC Four-stranded DNA Holliday Junction · 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 1ZF3 · PDBe 1ZF3

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