› 6d3o

X-ray diffraction
3.1Å resolution

Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-109) with HH4, an alpha/beta-Peptide with Irregular Secondary Structure

Released:
DOI: 10.2210/pdb6d3o/pdb
PDB entry 6d3o coloured by chain, front view.
PDB entry 6d3o coloured by chain, side view.
PDB entry 6d3o coloured by chain, top view.
Source organisms:
Entry authors: Thomas NC, Forest KT, Gellman SH

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-147427 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
N-VEGF Chain: A
Molecule details ›
Chain: A
Length: 102 amino acids
Theoretical weight: 11.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P15692 (Residues: 214-315; Coverage: 26%)
Gene names: VEGF, VEGFA
Sequence domains: VEGF heparin-binding domain
Structure domains: Cystine-knot cytokines
N-VEGF Chain: B
Molecule details ›
Chain: B
Length: 102 amino acids
Theoretical weight: 11.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P15692 (Residues: 214-315; Coverage: 26%)
Gene names: VEGF, VEGFA
Sequence domains: VEGF heparin-binding domain
Structure domains: Cystine-knot cytokines
HH4 alpha/beta-Peptide Chains: C, D
Molecule details ›
Chains: C, D
Length: 15 amino acids
Theoretical weight: 1.99 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
3 modified residues:
Ligand NLE 2 x NLE
Ligand HT7 2 x HT7
Ligand B3E 2 x B3E

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P63
Unit cell:
a: 101.649Å b: 101.649Å c: 59.988Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.219 0.217 0.279
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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