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Cricket paralysis virus igr ires domain 3 RNA bound to selenate, structure #2

Analyse Cricket paralysis virus igr ires domain 3 RNA bound to selenate, structure #2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MJA
Type: RNA
Length: 43 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Domain 3 of the cricket paralysis virus intergenic region ires RNA; RNA…
Ligands: SE4
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Domain 3 of the cricket paralysis virus intergenic region ires RNA	rna	29	—	—
C	RNA (5'-R(PUPAPAPGPAPAPAPUPUPUPAPCPCPU)-3')	rna	14	—	—

Ligands and binding sites

SE4 · Selenate ion · ion · 4 copies · chains B, C

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	303	0.49	0.74	25	empty

Interfaces

1 interface between chains.

B–C · 492 Å² buried · 36 hydrogen bonds · nucleic-nucleic

Compared structures

3MJA · Cricket Paralysis Virus IGR IRES Domain 3 RNA bound to selenate, structure #2 · 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 3MJA · PDBe 3MJA

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