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RNA duplex containing U-Ag-U base pairs

Analyse RNA duplex containing U-Ag-U base pairs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ECO
Type: RNA
Length: 72 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.81
Molecule: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
Ligands: AG
Pockets: 3 · best druggability 0.47

Structure

x-ray diffraction · resolution 1.81 · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, F, A, B, C, D	RNA (5'-R(GPGPGPUPCPCPGPGPUPCPCPC)-3')	rna	12	—	—

Ligands and binding sites

AG · Silver ion · metal · 6 copies · chains E, F, A, B, C, D

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

Pockets

3 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	292	0.47	0.73	18	empty
2	261	0.46	0.73	19	empty
3	204	0.42	0.73	15	empty

Interfaces

9 interfaces between chains.

A–B · 570 Å² buried · 52 hydrogen bonds · nucleic-nucleic
C–D · 565 Å² buried · 56 hydrogen bonds · nucleic-nucleic
E–F · 563 Å² buried · 56 hydrogen bonds · nucleic-nucleic
A–D · 114 Å² buried · 3 hydrogen bonds · nucleic-nucleic
B–C · 112 Å² buried · 3 hydrogen bonds · nucleic-nucleic

Compared structures

7ECO · RNA duplex containing U-ag-U base pairs · 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 7ECO · PDBe 7ECO

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