› 5o4e

X-ray diffraction
2.15Å resolution

Crystal structure of VEGF in complex with heterodimeric Fcab JanusCT6

Released:
DOI: 10.2210/pdb5o4e/pdb
PDB entry 5o4e coloured by chain, front view.
PDB entry 5o4e coloured by chain, side view.
PDB entry 5o4e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 Å crystal structure of the complex.
Lobner E, Humm AS, Mlynek G, Kubinger K, Kitzmüller M, Traxlmayr MW, Djinović-Carugo K, Obinger C
MAbs 9 1088-1104 (2017)
PMID: 28816592

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143679 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (7 distinct):
Immunoglobulin gamma-1 heavy chain Chain: A
Molecule details ›
Chain: A
Length: 223 amino acids
Theoretical weight: 25.18 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DOX5 (Residues: 227-449; Coverage: 50%)
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Immunoglobulin gamma-1 heavy chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 228 amino acids
Theoretical weight: 25.92 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DOX5 (Residues: 227-389, 390-449; Coverage: 50%)
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Immunoglobulin gamma-1 heavy chain Chain: C
Molecule details ›
Chain: C
Length: 222 amino acids
Theoretical weight: 25.05 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DOX5 (Residues: 227-448; Coverage: 49%)
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
N-VEGF Chains: E, F
Molecule details ›
Chains: E, F
Length: 96 amino acids
Theoretical weight: 11.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P15692 (Residues: 219-314; Coverage: 24%)
Gene names: VEGF, VEGFA
Structure domains: Cystine-knot cytokines

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand MPD 10 x MPD
Ligand MRD 1 x MRD
Ligand CAC 2 x CAC
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-1
Spacegroup: P212121
Unit cell:
a: 89.499Å b: 130.345Å c: 139.168Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.2 0.236
Expression systems:
  • Homo sapiens
  • Escherichia coli

Quick links

Citations

5 citation in other articles

Automatically Fixing Errors in Glycoprotein Structures with Rosetta.
Frenz et al. (2019)
4 more

2 mentions without citation

Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 Å crystal structure of the complex.
Lobner et al. (2017)
1 more