MolNFT v1 · #136675 · RNA

RNA duplex with 2-meimpg analogue bound-one binding site

5V0H · RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)…: “RNA duplex with 2-meimpg analogue bound-one binding site”. X-ray diffraction, 2 ligands (8OS, MG), 1 pocket (best druggability 0.49). MolNFT v1 #136675 on GenesisL1: 3D structure, binding…

PDB: 5V0H
Type: RNA
Length: 30 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*GP*G)-3')
Ligands: 8OS, 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)P(LCG) PAPCPUPUPAPAPGPUPCPGP*G)-3')	rna	15	—	—

Ligands and binding sites

8OS · 5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl) phosphoryl]guanosine · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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	0.49	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 691 Å² buried · 69 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

5V0H · RNA duplex with 2-MeImpG analogue bound-one binding site · 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 5V0H · PDBe 5V0H

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