› 3p9w

X-ray diffraction
2.41Å resolution

Crystal structure of an engineered human autonomous VH Domain in complex with VEGF

Released:
DOI: 10.2210/pdb3p9w/pdb
PDB entry 3p9w coloured by chain, front view.
PDB entry 3p9w coloured by chain, side view.
PDB entry 3p9w coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design of synthetic autonomous VH domain libraries and structural analysis of a VH domain bound to vascular endothelial growth factor.
Ma X, Barthelemy PA, Rouge L, Wiesmann C, Sidhu SS
J Mol Biol 425 2247-59 (2013)
PMID: 23507309

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-210640 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-VEGF Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 106 amino acids
Theoretical weight: 12.42 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P15692 (Residues: 215-318; Coverage: 26%)
Gene names: VEGF, VEGFA
Sequence domains: VEGF heparin-binding domain
Structure domains: Cystine-knot cytokines
human VEGF Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 123 amino acids
Theoretical weight: 13.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 52.727Å b: 132.908Å c: 175.481Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.193 0.233
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

3 review citations

Mutational approaches to improve the biophysical properties of human single-domain antibodies.
Kim et al. (2014)
2 more

5 mentions without citation

Engineered Autonomous Human Variable Domains.
Nilvebrant et al. (2016)
4 more