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RNA-monomer complex containing pyrophosphate linkage

Analyse RNA-monomer complex containing pyrophosphate linkage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6U6J
Type: RNA
Length: 28 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(DPG))-3')
Ligands: GDP, EQ4
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (5'-R((LCC)P(LCC)P(LCC)P(LCG) PAPCPUPUPAPAPGPUPCPG*(DPG))-3')	rna	14	—	—

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
EQ4 · 5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy) phosphoryl]guanosine · ligand · 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	303	0.48	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 576 Å² buried · 45 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 modified, 2 covalent (nucleotide modification, covalent ligand).

Compared structures

6U6J · RNA-monomer complex containing pyrophosphate linkage · 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 6U6J · PDBe 6U6J

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