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Crystal structure of 1NT-5'-overhanging double-helical ccg-repetitive RNA 20MER complexed with rss P19

Analyse Crystal structure of 1NT-5'-overhanging double-helical ccg-repetitive RNA 20MER… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KNQ
Type: protein + RNA
Length: 142 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(P*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*G P*CP*G)-3'; RNA silencing…
UniProt: P69517
Ligands: SO4
Pockets: 1 · best druggability 0.33

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-R(PCPCPGPCPCPGPCPCPGPCPCPGPCPCPGPCPCPG PCPG)-3'	rna	20	—	—
A	RNA silencing suppressor P19	protein	122	38% helix, 26% strand	P69517

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies

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	107	0.33	0.72	24	empty

Interfaces

1 interface between chains.

B–A · 664 Å² buried · 22 hydrogen bonds · protein-nucleic

Compared structures

4KNQ · Crystal structure of 1nt-5'-overhanging double-helical CCG-repetitive RNA 20mer complexed… · 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
Every structure of UniProt P69517
Elsewhere: RCSB PDB 4KNQ · PDBe 4KNQ · UniProt P69517

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