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Crystal structure of hepatitis C virus ires subdomain iia

Analyse Crystal structure of hepatitis C virus ires subdomain iia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PN3
Type: RNA
Length: 44 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'- R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP *AP*CP*GP*CP*C)-3'…
Ligands: MG
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'- R(CPGPGPAPGPGPAPAPCPUPAPCPUPGPUPCPUPUPCP APCPGPCPC)-3'	rna	24	—	—
B	5'-R(GPCPGP(5BU) PGPUPCPGPUPGPCPAPGPCPCP(5BU)PCPCPGPG)-3'	rna	20	—	—

Ligands and binding sites

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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	425	0.58	0.75	30	MG

Interfaces

1 interface between chains.

A–B · 1075 Å² buried · 115 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

2PN3 · Crystal Structure of Hepatitis C Virus IRES Subdomain IIa · 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 2PN3 · PDBe 2PN3

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