Brand  (β version)

color scheme of protein:

hetatm:

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information
centroid:
interaction residue:

chain: Hide other chain(s)

Ligands
Code Name Link
MG Magnesium ion
NA Sodium ion
Modified Residues
Code Name Link
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)
PE6 Phosphoryl-hexaethylene glycol
UPE 2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
Code : 4HQU
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

PubMed: 23139410
DOI: 10.1073/pnas.1213933109

Chain : A
UniProt : P01127 (PDGFB_HUMAN)
Reaction : -