Het-PDB Navi2 (PDB: 4HQU)

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Ligands
Code	Name		Style	Show	Link
MG	Magnesium ion				PoSSuM
NA	Sodium ion				PoSSuM

Non-standard Residues
Code	Name	Show
18M	2'-O-methylguanosine 3',5'-bis(dihydrogen phosphate)
18Q	2'-deoxy-5-[(thiophen-2-ylmethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
A2M	2'-O-methyladenosine 5'-(dihydrogen phosphate)
DUZ	5-(benzylcarbamoyl)-2'-deoxyuridine 5'-(dihydrogen phosphate)
UPE	2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show
PE6	Phosphoryl-hexaethylene glycol

Download interaction data: 4HQU

Code :

4HQU PDBj RCSB PDB PDBe

Header :

HORMONE/DNA

Title :

Crystal structure of human PDGF-BB in complex with a modified nucleotide aptamer (SOMAmer SL5)

Release Data :

2012-11-21

Compound :

mol_id	molecule	chains	synonym
1	Platelet-derived growth factor subunit B	A	PDGF subunit B, PDGF-2, Platelet-derived growth factor B chain, Platelet-derived growth factor beta polypeptide, Proto-oncogene c-Sis
	fragment: PDGF-BB, UNP residues 82-109

mol_id	molecule	chains
2	SOMAmer SL5	C

Source :

mol_id	organism_scientific	organism_common	expression_system
1	Homo sapiens (taxid:9606)	Human	Escherichia coli (taxid:562)
	gene: PDGFB, PDGF2, SIS

mol_id	organism_scientific
2
	synthetic: yes other_details: Synthesized oligonucleotide

Authors :

Davies, D.R., Edwards, T.E., Janjic, N., Gelinas, A.D., Zhang, C., Jarvis, T.C.

Keywords :

Growth factor, SELEX, aptamer, 5-modified deoxyuridine, HORMONE-DNA complex

Exp. method :

X-RAY DIFFRACTION ( 2.20 Å )

Citation :

Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.

Davies, D.R.,Gelinas, A.D.,Zhang, C. et al.
(2012) Proc.Natl.Acad.Sci.USA 109 : 19971 - 19976

PDB ID: 4HQU