MolNFT v1 · #72839 · RNA

A 1.9A crystal structure of the hdv ribozyme precleavage suggests both lewis acid and general acid mechanisms contribute to phosphodiester cleavage

3NKB · DNA/RNA (5'-D(*(DUR))-D(*GP*G)-R(P*CP*UP*UP*GP*CP*A)-3'): “A 1.9A crystal structure of the hdv ribozyme precleavage suggests both lewis acid and general acid mechanisms…”. X-ray diffraction, 1 ligand (MG), 3 pockets (best…

PDB: 3NKB
Type: RNA
Length: 72 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA/RNA (5'-D(*(DUR))-D(*GP*G)-R(P*CP*UP*UP*GP*CP*A)-3'); The hepatitis delta virus…
Ligands: MG
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA/RNA (5'-D((DUR))-D(GPG)-R(PCPUPUPGPCP*A)-3')	rna	8	—	—
B	The hepatitis delta virus ribozyme	rna	64	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 10 copies · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.66	0.78	30	MG
2	351	0.51	0.74	20	empty
3	111	0.42	0.78	14	MG

Interfaces

1 interface between chains.

A–B · 507 Å² buried · 40 hydrogen bonds · nucleic-nucleic

Compared structures

3NKB · A 1.9A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and… · 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 3NKB · PDBe 3NKB

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