MolNFT v1 · #115460 · DNA + RNA

Crystal structure of 9DB1* deoxyribozyme (cobalt hexammine soaked crystals)

5CKI · RNA (5'-R(P*GP*CP*AP*CP*UP*AP*GP*AP*UP*CP*GP*GP*AP*UP*G)…: “Crystal structure of 9DB1* deoxyribozyme (cobalt hexammine soaked crystals)”. X-ray diffraction, 2 ligands (CO, MG), 2 pockets (best druggability 0.41). MolNFT v1 #115460…

PDB: 5CKI
Type: DNA + RNA
Length: 59 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(P*GP*CP*AP*CP*UP*AP*GP*AP*UP*CP*GP*GP*AP*UP*G)- 3'); DNA (44-mer)
Ligands: CO, MG
Pockets: 2 · best druggability 0.41

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	RNA (5'-R(PGPCPAPCPUPAPGPAPUPCPGPGPAPUP*G)- 3')	rna	15	—	—
Y	DNA (44-mer)	dna	44	—	—

Ligands and binding sites

CO · Cobalt (II) ion · metal · 4 copies · chains D, Y
MG · Magnesium ion · metal · 2 copies · chains Y

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

Pockets

2 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	157	0.41	0.75	13	empty
2	62	0.30	0.76	9	MG

Interfaces

1 interface between chains.

D–Y · 1185 Å² buried · 87 hydrogen bonds · nucleic-nucleic

Compared structures

5CKI · Crystal structure of 9DB1* deoxyribozyme (Cobalt hexammine soaked crystals) · 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 5CKI · PDBe 5CKI

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