Research workbench

Octameric RNA duplex soaked in COPPER(II)CHLORIDE

Analyse Octameric RNA duplex soaked in COPPER(II)CHLORIDE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4U78
Type: RNA
Length: 16 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*UP*CP*GP*UP*AP*CP*GP*A)-3')
Ligands: CU, CA
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	RNA (5'-R(UPCPGPUPAPCPGPA)-3')	rna	8	—	—

Ligands and binding sites

CU · Copper (II) ion · metal · 2 copies · chains B, A
CA · Calcium ion · metal · 2 copies · chains B, A

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

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	92	0.35	0.76	12	CU, CA

Interfaces

1 interface between chains.

B–A · 444 Å² buried · 36 hydrogen bonds · nucleic-nucleic

Compared structures

4U78 · Octameric RNA duplex soaked in copper(II)chloride · the same entry in another collection · chain B against B, 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 4U78 · PDBe 4U78

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