› 4gln

X-ray diffraction
1.6Å resolution

Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21/n

Released:
DOI: 10.2210/pdb4gln/pdb
PDB entry 4gln coloured by chain, front view.
PDB entry 4gln coloured by chain, side view.
PDB entry 4gln coloured by chain, top view.
Source organisms:
Primary publication:
Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography.
Mandal K, Uppalapati M, Ault-Riché D, Kenney J, Lowitz J, Sidhu SS, Kent SB
Proc Natl Acad Sci U S A 109 14779-84 (2012)
PMID: 22927390

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-147437 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-VEGF Chains: E, F
Molecule details ›
Chains: E, F
Length: 102 amino acids
Theoretical weight: 11.95 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P15692 (Residues: 214-315; Coverage: 26%)
Gene names: VEGF, VEGFA
Sequence domains: VEGF heparin-binding domain
Structure domains: Cystine-knot cytokines
D-RFX001 Chains: D, H
Molecule details ›
Chains: D, H
Length: 56 amino acids
Theoretical weight: 6.38 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
13 modified residues:
Ligand DTH 20 x DTH
Ligand DTY 6 x DTY
Ligand DLY 8 x DLY
Ligand DLE 6 x DLE
Ligand DIL 2 x DIL
Ligand DSG 4 x DSG
Ligand DGL 6 x DGL
Ligand DAL 10 x DAL
Ligand DVA 10 x DVA
Ligand DAS 16 x DAS
Ligand DPN 14 x DPN
Ligand DSN 4 x DSN
Ligand DTR 2 x DTR

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Unit cell:
a: 57.156Å b: 88.322Å c: 77.866Å
α: 90° β: 99.98° γ: 90°
R-values:
R R work R free
0.23 0.229 0.264
Expression system: Not provided

Quick links

Citations

11 review citations

Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins.
Bondalapati et al. (2016)
10 more

8 mentions without citation

Biosynthesis of GPI-anchored proteins: special emphasis on GPI lipid remodeling.
Kinoshita et al. (2016)
7 more