MolNFT v1 · #29084 · RNA

HIV-1 dis RNA subtype F- zn soaked

1YXP · 5'-R(*CP*UP*(5BU) P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*C…: “HIV-1 dis RNA subtype F- zn soaked”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.62). MolNFT v1 #29084 on GenesisL1: 3D structure, binding sites and…

PDB: 1YXP
Type: RNA
Length: 46 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*CP*UP*(5BU) P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP* G)-3'
Ligands: ZN
Pockets: 1 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-R(CPUP(5BU) PGPCPUPGPAPAPGPUPGPCPAPCPAPCPAPGPCPAPAP* G)-3'	rna	23	—	—

Ligands and binding sites

ZN · Zinc 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	717	0.62	0.74	38	ZN

Interfaces

1 interface between chains.

A–B · 373 Å² buried · 36 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

1YXP · HIV-1 DIS RNA subtype F- Zn soaked · 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 1YXP · PDBe 1YXP

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