MolNFT v1 · #136677 · RNA

RNA duplex with 2-meimpg analogue bound-2 binding sites

5V0J · RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)…: “RNA duplex with 2-meimpg analogue bound-2 binding sites”. X-ray diffraction, 2 ligands (8OS, MG), 1 pocket (best druggability 0.48). MolNFT v1 #136677 on GenesisL1: 3D structure, binding…

PDB: 5V0J
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*(LCA)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
Ligands: 8OS, MG
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(LCA)P(LCG) PAPCPUPUPAPAPGPUPCPU)-3')	rna	14	—	—

Ligands and binding sites

8OS · 5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl) phosphoryl]guanosine · ligand · 4 copies · chains A, B
MG · Magnesium ion · metal

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	316	0.48	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 538 Å² buried · 43 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 modified (nucleotide modification).

Compared structures

5V0J · RNA duplex with 2-MeImpG analogue bound-2 binding sites · 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 5V0J · PDBe 5V0J

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