Research workbench

1.9 a resolution X-ray structure of (GGCAGCAGCC)2

Analyse 1.9 a resolution X-ray structure of (GGCAGCAGCC)2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NJ7
Type: RNA
Length: 60 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'
Ligands: SO4
Pockets: 1 · best druggability 0.29

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	5'-R(GPGPCPAPGPCPAPGPCPC)-3'	rna	10	—	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F

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	63	0.29	0.75	11	empty

Interfaces

9 interfaces between chains.

C–D · 498 Å² buried · 37 hydrogen bonds · nucleic-nucleic
E–F · 497 Å² buried · 41 hydrogen bonds · nucleic-nucleic
A–B · 492 Å² buried · 41 hydrogen bonds · nucleic-nucleic
B–E · 105 Å² buried · 2 hydrogen bonds · nucleic-nucleic
B–F · 104 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Compared structures

3NJ7 · 1.9 A resolution X-ray structure of (GGCAGCAGCC)2 · 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 3NJ7 · PDBe 3NJ7

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