Het-PDB Navi2 (PDB: 6YCS)

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Ligands
Code	Name		Style	Show	Link
NA	Sodium ion				PoSSuM
SO4	Sulfate ion				PoSSuM

Non-standard Residues
Code	Name	Show
AS	2-deoxy-adenosine -5'-thio-monophosphate
GS	Guanosine-5'-thio-monophosphate
OKN	5'-methyl-2'-deoxycytidine-5'-phosphorothioate
OKQ	2'-O-methylcytidine-5'-phosphorothioate
OKT	2'-O-methyluridine-5'-phosphorothioate
PST	Thymidine-5'-thiophosphate
RFJ	2'-O-methyl-5'-O-thiophosphonoguanosine

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show
PPS	3'-phosphate-adenosine-5'-phosphate sulfate

Download interaction data: 6YCS

Code :

6YCS PDBj RCSB PDB PDBe

Header :

TRANSCRIPTION

Title :

Human Transcription Cofactor PC4 DNA-binding domain in complex with full phosphorothioate 5-10-5 2'-O-methyl DNA gapmer antisense oligonucleotide.

Release Data :

2020-04-29

Compound :

mol_id	molecule	chains	synonym
1	PC4 protein	A,B,C,D	SUB1 homolog (S. cerevisiae),isoform CRA_a,cDNA,FLJ92014,highly similar to Homo sapiens SUB1 homolog (S. cerevisiae) (SUB1),mRNA

mol_id	molecule	chains
2	DNA (5'-D(P(OKQ))-D(P(OKT))-R(P(RFJ))-D((OKQ)P(OKT)P(AS)P(GS)P(OKN)P(OKN)P(PST)P(OKN)P(PST)P(GS)P(GS)P(AS)P(OKT)P*(OKT))-3')	E

mol_id	molecule	chains
3	DNA (5'-D(P(OKQ))-D(P(OKT))-R(P(RFJ))-D((OKQ)P(OKT)P(AS)P(GS)P(OKN)P(OKN)P(PST)P(OKN)P(PST)P(GS)P(GS)P(AS)P(OKT)P*(OKT))-3')	F

Source :

mol_id	organism_scientific	organism_common	expression_system
1	Homo sapiens (taxid:9606)	Human	Escherichia coli BL21(DE3) (taxid:469008)
	gene: PC4, SUB1, hCG_1781938 expression_system_vector_type: plasmid expression_system_plasmid: pET15b

mol_id	organism_scientific
2	Synthetic construct (taxid:32630)
	synthetic: yes

mol_id	organism_scientific
3	Synthetic construct (taxid:32630)
	synthetic: yes

Authors :

Hyjek-Skladanowska, M., Vickers, T.A., Napiorkowska, A., Anderson, B., Tanowitz, M., Crooke, S.T., Liang, X., Seth, P.P., Nowotny, M.

Keywords :

DNA binding, phosphorothioate DNA, 2'-O-methyl, ASO, TRANSCRIPTION

Exp. method :

X-RAY DIFFRACTION ( 3.05 Å )

Citation :

Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins.

Hyjek-Skladanowska, M.,Vickers, T.A.,Napiorkowska, A. et al.
(2020) J.Am.Chem.Soc. 142 : 7456 - 7468

PDB ID: 6YCS