3NKB: A 1.9A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage

PDB ID: 3NKBDownload
MMDB ID: 84572
PDB Deposition Date: 2010/6/18
Updated in MMDB: 2023/09
Experimental Method:
x-ray diffraction
Resolution: 1.916  Å
Source Organism:
Biological Unit for 3NKB: dimeric; determined by author and by software (PISA)
Molecular Components in 3NKB
Label Count Molecule
Nucleotide(1 molecule)
1
the Hepatitis Delta Virus Ribozyme
Molecule annotation
Chemicals and Non-standard biopolymers (11 molecules)
A
1
DNA/RNA (5'-D(*(DUR))-D(*GP*G)-R(P*CP*UP*UP*GP*CP*A)-3')
1
10
MAGNESIUM IONMAGNESIUM ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303