MolNFT v1 · #169824 · DNA

Self-assembly of a 3D DNA crystal lattice (4X6 junction version) containing the J31 immobile holliday junction

6XO8 · DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*AP*GP*A)-3'): “Self-assembly of a 3D DNA crystal lattice (4X6 junction version) containing the J31 immobile holliday junction”. X-ray diffraction, 1 pocket (best druggability 0.39). MolNFT v1…

PDB: 6XO8
Type: DNA
Length: 42 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*AP*GP*A)-3'); DNA…
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'-D(GPAPGPCPAPGPAPCPCPAPGPA)-3')	dna	12	—	—
B	DNA (5'-D(PCPGPGPCPAPCPTPCP*A)-3')	dna	9	—	—
C	DNA (5'-D(PTPCPTPCPCPG)-3')	dna	6	—	—
D	DNA (5'-D(TPCPTPGPAPGPTPGPGPGPTPCPTPGP*C)- 3')	dna	15	—	—

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	183	0.39	0.73	17	empty

Interfaces

6 interfaces between chains.

A–D · 334 Å² buried · 23 hydrogen bonds · nucleic-nucleic
B–D · 295 Å² buried · 19 hydrogen bonds · nucleic-nucleic
C–D · 247 Å² buried · 11 hydrogen bonds · nucleic-nucleic
B–C · 150 Å² buried · 7 hydrogen bonds · nucleic-nucleic
A–C · 117 Å² buried · 6 hydrogen bonds · nucleic-nucleic

Compared structures

6XO8 · Self-assembly of a 3D DNA crystal lattice (4x6 junction version) containing the J31… · 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 6XO8 · PDBe 6XO8

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