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Structure of the G6 Fab, a phage derived Fab fragment, in complex with VEGF

X-ray diffraction
2.8Å resolution
PDB entry 2fjg coloured by chain, front view.
PDB entry 2fjg coloured by chain, side view.
PDB entry 2fjg coloured by chain, top view.
Source organism: Homo sapiens
Assemblies composition:
hetero hexamer (preferred)
hetero dodecamer
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Vascular endothelial growth factor A complex and antibody
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Multimeric state: hetero hexamer
Accessible surface area: 46001.96 Å2
Buried surface area: 14878.86 Å2
Dissociation area: 3,235.89 Å2
Dissociation energy (ΔGdiss): 25.56 kcal/mol
Dissociation entropy (TΔSdiss): 38.91 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-210645
Assembly 2
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Assembly Name: N-VEGF and IG-light kappa chain and IG-heavy chain
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Multimeric state: hetero dodecamer
Accessible surface area: 89282.74 Å2
Buried surface area: 32488.85 Å2
Dissociation area: 1,364.08 Å2
Dissociation energy (ΔGdiss): 7.98 kcal/mol
Dissociation entropy (TΔSdiss): 16.61 kcal/mol
Symmetry number: 4
PDBe Complex ID: PDB-CPX-210655

Macromolecules

N-VEGF
Chains: V, W
Length: 102 amino acids
Theoretical weight: 11.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P15692 (Residues: 214-315; Coverage: 26%)
Gene names: VEGF, VEGFA
Pfam: VEGF heparin-binding domain
InterPro:
CATH: Cystine-knot cytokines
SCOP: Platelet-derived growth factor-like
N-VEGF in PDB entry 2fjg, assembly 1, front view.
N-VEGF in PDB entry 2fjg, assembly 1, side view.
N-VEGF in PDB entry 2fjg, assembly 1, top view.
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Fab light chain
Chains: A, L
Length: 214 amino acids
Theoretical weight: 23.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
InterPro:
CATH: Immunoglobulins
Fab light chain in PDB entry 2fjg, assembly 1, front view.
Fab light chain in PDB entry 2fjg, assembly 1, side view.
Fab light chain in PDB entry 2fjg, assembly 1, top view.
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Fab heavy chain
Chains: B, H
Length: 227 amino acids
Theoretical weight: 24.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
InterPro:
CATH: Immunoglobulins
SCOP:
Fab heavy chain in PDB entry 2fjg, assembly 1, front view.
Fab heavy chain in PDB entry 2fjg, assembly 1, side view.
Fab heavy chain in PDB entry 2fjg, assembly 1, top view.
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