Research workbench

Crystal structure of an RNA-5'/DNA-3' strand exchange junction

Analyse Crystal structure of an RNA-5'/DNA-3' strand exchange junction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7THB
Type: DNA + RNA
Length: 78 nucleotides
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*TP*AP*AP*GP*CP*AP*GP*CP*AP*TP*C)-3'); RNA (5'-R(*AP*GP*CP*UP*UP*AP*C)-3')…
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G	DNA (5'-D(GPTPAPAPGPCPAPGPCPAPTPC)-3')	dna	12	—	—
B, E, H	RNA (5'-R(APGPCPUPUPAP*C)-3')	rna	7	—	—
C, F, I	DNA (5'-D(GPAPTPGPCPTP*C)-3')	dna	7	—	—

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	310	0.49	0.73	21	empty

Interfaces

20 interfaces between chains.

G–H · 305 Å² buried · 28 hydrogen bonds · nucleic-nucleic
D–E · 298 Å² buried · 29 hydrogen bonds · nucleic-nucleic
A–B · 292 Å² buried · 32 hydrogen bonds · nucleic-nucleic
D–F · 278 Å² buried · 29 hydrogen bonds · nucleic-nucleic
A–C · 271 Å² buried · 24 hydrogen bonds · nucleic-nucleic

Compared structures

7THB · Crystal structure of an RNA-5'/DNA-3' strand exchange junction · the same entry in another collection · chain D against D, 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 7THB · PDBe 7THB

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.