MolNFT v1 · #135955 · RNA

RNA primer-template complex with guanosine dinucleotide ligand G(5') PPP(5')G

5UEE · RNA (5'-R(*(LCC)P*(LCC)P*(LCC) P*GP*AP*CP*UP*UP*AP*AP*GP*UP*…: “RNA primer-template complex with guanosine dinucleotide ligand G(5') PPP(5')G”. X-ray diffraction, 2 ligands (GP3, MG), 1 pocket (best druggability 0.49). MolNFT v1…

PDB: 5UEE
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*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
Ligands: GP3, MG
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

GP3 · Diguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 6 copies

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	341	0.49	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 594 Å² buried · 57 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 6 modified (nucleotide modification).

Compared structures

5UEE · RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G · 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 5UEE · PDBe 5UEE

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