MolNFT v1 · #149890 · DNA

Holliday junctions formed from telomeric DNA

6GDH · DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3'): “Holliday junctions formed from telomeric DNA”. X-ray diffraction, 3 pockets (best druggability 0.33). MolNFT v1 #149890 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GDH
Type: DNA
Length: 80 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3'); DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
Pockets: 3 · best druggability 0.33

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	DNA (5'-D(CPTPAPAPCPCPCPTPAPA)-3')	dna	10	—	—
B, D, F, H	DNA (5'-D(TPTPAPGPGPGPTPTPAPG)-3')	dna	10	—	—

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	115	0.33	0.72	17	empty
2	81	0.31	0.74	12	empty
3	51	0.24	0.73	9	empty

Interfaces

10 interfaces between chains.

F–G · 289 Å² buried · 29 hydrogen bonds · nucleic-nucleic
A–D · 286 Å² buried · 29 hydrogen bonds · nucleic-nucleic
E–H · 279 Å² buried · 28 hydrogen bonds · nucleic-nucleic
B–C · 278 Å² buried · 30 hydrogen bonds · nucleic-nucleic
A–C · 228 Å² buried · 7 hydrogen bonds · nucleic-nucleic

Compared structures

6GDH · Holliday Junctions formed from Telomeric DNA · 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 6GDH · PDBe 6GDH

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