Het-PDB Navi2 (PDB: 5DO4)

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Ligands
Code	Name	Link
0G6	D-phenylalanyl-N-[(2s,3s)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide	PoSSuM
CA	Calcium ion	PoSSuM
EDO	1,2-ethanediol	PoSSuM
GOL	Glycerol	PoSSuM
MG	Magnesium ion	PoSSuM
MRD	(4r)-2-methylpentane-2,4-diol	PoSSuM

Non-standard Residues
Code	Name	Show
CFZ	2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate)
UFT	2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate)
UMS	2'-methylselenyl-2'-deoxyuridine-5'-phosphate

Glycosylation
Code	Name	Emphasize
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose

Modification
Code	Name	Show
ADS	Adenosine-5'-(dithio)phosphate

Download interaction data: 5DO4

Code :

5DO4 PDBj RCSB PDB PDBe

Header :

Hydrolase/RNA

Title :

Thrombin-RNA aptamer complex

Release Data :

2016-09-14

Compound :

mol_id	molecule	chains	synonym
1	Thrombin light chain	L	Coagulation factor II
	ec: 3.4.21.5

mol_id	molecule	chains	synonym
2	Thrombin heavy chain	H	Coagulation factor II
	ec: 3.4.21.5

mol_id	molecule	chains
3	RNA (25-MER)	A

Source :

mol_id	organism_scientific	organism_common
1	Homo sapiens (taxid:9606)	Human

mol_id	organism_scientific	organism_common
2	Homo sapiens (taxid:9606)	Human

mol_id	organism_scientific
3	Unidentified (taxid:32644)
	synthetic: yes

Authors :

Pallan, P.S., Egli, M.

Keywords :

Thrombin-RNA aptamer, phosphorodithioate RNA, PS2-RNA, PS2 linkage, Hydrolase-RNA complex

Exp. method :

X-RAY DIFFRACTION ( 1.8590 Å )

Citation :

Evoking picomolar binding in RNA by a single phosphorodithioate linkage.

Abeydeera, N.D.,Egli, M.,Cox, N. et al.
(2016) Nucleic Acids Res. 44 : 8052 - 8064

PDB ID: 5DO4