› 4hqx

X-ray diffraction
2.3Å resolution

CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)

Released:
DOI: 10.2210/pdb4hqx/pdb
PDB entry 4hqx coloured by chain, front view.
PDB entry 4hqx coloured by chain, side view.
PDB entry 4hqx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.
Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter JD, O'Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis TC
Proc Natl Acad Sci U S A 109 19971-6 (2012)
PMID: 23139410

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117609 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Platelet-derived growth factor subunit B Chain: A
Molecule details ›
Chain: A
Length: 102 amino acids
Theoretical weight: 11.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01127 (Residues: 82-183; Coverage: 46%)
Gene names: PDGF2, PDGFB, SIS
Sequence domains: PDGF/VEGF domain
Structure domains: Cystine-knot cytokines
SOMAmer SL4 Chain: C
Molecule details ›
Chain: C
Length: 24 nucleotides
Theoretical weight: 8.53 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NA 1 x NA
Ligand MG 1 x MG
6 modified residues:
Ligand DUZ 5 x DUZ
Ligand A2M 3 x A2M
Ligand UBI 1 x UBI
Ligand UPE 1 x UPE
Ligand 18Q 1 x 18Q
Ligand 18M 1 x 18M

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P41212
Unit cell:
a: 59.43Å b: 59.43Å c: 168.16Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.239 0.279
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

34 review citations

Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents.
Rohloff et al. (2014)
33 more

4 mentions without citation

Structural Biology for the Molecular Insight between Aptamers and Target Proteins.
Zhang et al. (2021)
3 more