4HQU: Human PDGF-BB

Crystal structure of human PDGF-BB in complex with a modified nucleotide aptamer (SOMAmer SL5). Determined by X-ray diffraction at 2.2 Å resolution. Released 21 Nov 2012.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,382
Mol. weight: 20.92 kDa
Ligands: MG
Released: 21 Nov 2012

Explore 4HQU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HQU contains 3 α-helices and 5 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	17-24	8	1
α-helix	25-26	2
α-helix	27-30	4
β-strand	37-40	4	2
β-strand	43-50	8	1
β-strand	59-78	20	2
β-strand	81-100	20	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Platelet-derived growth factor subunit B	A	protein	109	Homo sapiens	P01127 (AlphaFold model)
SOMAmer SL5	C	DNA	24

Sequence of entity 1 (A), FASTA

>4HQU_1 Platelet-derived growth factor subunit B (chains A)
SLGSLTIAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQC
RPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETVAAARPVT

Sequence of entity 2 (C), FASTA

>4HQU_2 SOMAmer SL5 (chains C)
XXACXGXXACACGCGXXXAXAGCX

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Water and common crystallization additives (NA) are not listed.

Primary 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. Proc Natl Acad Sci U S A (2012) 109:19971-19976. DOI 10.1073/pnas.1213933109 · PubMed

Other PDB entries of the same protein (UniProt P01127 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MJG 2.3 Å, The structure of a platelet derived growth factor receptor complex
4HQX 2.3 Å, CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer…
4QCI 2.3 Å, PDGF-B blocking antibody bound to PDGF-BB
6T9E 2.99 Å, Crystal structure of a bispecific DutaFab in complex with human PDGF
1PDG 3.0 Å, Crystal structure of human platelet-derived growth factor bb

Browse structure collections

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