6d3o

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

Method: X-RAY DIFFRACTION D_max: 74.2 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vascular endothelial growth factor A

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 34–135 Chain B； UniProt 34–135	Fragment：residues 34-135	HH4 alpha/beta-Peptide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v PEG 10000	Resolution 3.10 Å R-free 0.279

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6D3O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BJ1 VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY Deposited 1998-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain V 214–315（102 aa） Fragment：RECEPTOR BINDING DOMAIN Chain W 214–315（102 aa） Fragment：RECEPTOR BINDING DOMAIN	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.40 Å R-free 0.266
1CZ8 VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH AN AFFINITY MATURED ANTIBODY Deposited 1999-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain V 40–133（94 aa） Fragment：RECEPTOR BINDING FRAGMENT Chain W 40–133（94 aa） Fragment：RECEPTOR BINDING FRAGMENT	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 4000, ISOPROPANOL, AMMONIUM SULFATE, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
1FLT VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1997-11-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 38–135（98 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109 Chain W 38–135（98 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.70 Å R-free 0.261
1FLT VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1997-11-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain V 38–135（98 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109 Chain W 38–135（98 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.70 Å R-free 0.261
1KAT Solution Structure of a Phage-Derived Peptide Antagonist in Complex with Vascular Endothelial Growth Factor Deposited 2001-11-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 37–135（99 aa） Fragment：Receptor Binding Domain Chain W 37–135（99 aa） Fragment：Receptor Binding Domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 50mM sodium chloride, 20 sodium phosphate；Pressure 1 NMR measurement conditions pH 7；318 K；Ionic strength (raw mmCIF value) 50mM sodium chloride, 20 sodium phosphate；Pressure 1 NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50mM sodium chloride, 20 sodium phosphate；Pressure 1 NMR sample composition 0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide \| 90% H2O/10% D2O NMR sample composition 0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide \| 100% D2O NMR sample composition 1.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide \| 90% H2O/10% D2O NMR sample composition 1.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide \| 100% D2O NMR sample composition 0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide, 15mg/ml pf1 phage \| 90% H2O/10% D2O NMR sample composition 1.0mM U-13C/15N labeled VEGF Dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide, 15mg/ml pf1 phage \| 90% H2O/10% D2O	Resolution not provided
1KMX Heparin-binding Domain from Vascular Endothelial Growth Factor Deposited 2001-12-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 137–191（55 aa） Fragment：heparin-binding domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 25 mM sodium acetate; 50 mM sodium chloride；Pressure ambient NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 25 mM sodium acetate; 50 mM sodium chloride；Pressure ambient NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 25 mM sodium acetate; 50 mM sodium chloride；Pressure ambient NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 25 mM sodium acetate; 50 mM sodium chloride；Pressure ambient NMR sample composition 2.0 mM VEGF heparin-binding domain; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide \| 90% H2O/10% D2O NMR sample composition 2.0 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide \| 90% H2O/10% D2O NMR sample composition 2.0 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide \| 99.9% D2O NMR sample composition 0.6 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride; 0.02% sodium azide \| 4:1:0.2 ditridecanoyl-phosphatidylcholine/dihexanoyl-phosphatidylcholine/cetyltrimethylammonium bromide, 5% w/v total lipid in 90% H2O, 10% D2O	Resolution not provided
1MJV DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A (C51A and C60A) Deposited 2002-08-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 40–134（95 aa） Fragment：Residues 40-134, Sequence Database Chain B 40–134（95 aa） Fragment：Residues 40-134, Sequence Database	Mutation：C51A,C60A Mutation：C51A,C60A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；Na-Citrate, isopropanol, PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.248
1MKG DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A (C57A and C102A) Deposited 2002-08-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 40–134（95 aa） Fragment：Residues 40-134, sequence database Chain B 40–134（95 aa） Fragment：Residues 40-134, sequence database	Mutation：C57A,C102A Mutation：C57A,C102A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Na-formate 2.0 M, Na-acetate 0.1 M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.288
1MKG DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A (C57A and C102A) Deposited 2002-08-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 40–134（95 aa） Fragment：Residues 40-134, sequence database Chain D 40–134（95 aa） Fragment：Residues 40-134, sequence database	Mutation：C57A,C102A Mutation：C57A,C102A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Na-formate 2.0 M, Na-acetate 0.1 M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.288
1MKG DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A (C57A and C102A) Deposited 2002-08-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 40–134（95 aa） Fragment：Residues 40-134, sequence database Chain B 40–134（95 aa） Fragment：Residues 40-134, sequence database Chain C 40–134（95 aa） Fragment：Residues 40-134, sequence database Chain D 40–134（95 aa） Fragment：Residues 40-134, sequence database	Mutation：C57A,C102A Mutation：C57A,C102A Mutation：C57A,C102A Mutation：C57A,C102A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Na-formate 2.0 M, Na-acetate 0.1 M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.288
1MKK Disulfide deficient mutant of vascular endothelial growth factor A (C61A and C104A) Deposited 2002-08-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 40–134（95 aa） Fragment：Residues 40-134, sequence database Chain B 40–134（95 aa） Fragment：Residues 40-134, sequence database	Mutation：C61A,C104A Mutation：C61A,C104A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；isopropanol, PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.32 Å R-free 0.195
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN Chain W 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.284
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN Chain S 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.284
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain R 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN Chain S 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN Chain V 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN Chain W 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.284
1TZH Crystal Structure of the Fab YADS1 Complexed with h-VEGF Deposited 2004-07-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain V 34–135（102 aa） Chain W 34–135（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；PEG 3350, ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.60 Å R-free 0.271
1TZI Crystal Structure of the Fab YADS2 Complexed with h-VEGF Deposited 2004-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain V 34–135（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；292 K；LITHIUM CHLORIDE, PEG 6000, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.80 Å R-free 0.254
1VGH HEPARIN-BINDING DOMAIN FROM VASCULAR ENDOTHELIAL GROWTH FACTOR, NMR, 20 STRUCTURES Deposited 1997-12-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 161–215（55 aa） Fragment：HEPARIN-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；300 K	Resolution not provided
1VPF STRUCTURE OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR Deposited 1997-04-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109 Chain B 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.50 Å R-free 0.297
1VPF STRUCTURE OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR Deposited 1997-04-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109 Chain D 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.50 Å R-free 0.297
1VPP COMPLEX BETWEEN VEGF AND A RECEPTOR BLOCKING PEPTIDE Deposited 1998-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN Chain W 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.90 Å R-free 0.270
2QR0 Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs Deposited 2007-07-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 39–135（97 aa） Chain D 39–135（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å R-free 0.312
2QR0 Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs Deposited 2007-07-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 39–135（97 aa） Chain J 39–135（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å R-free 0.312
2QR0 Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs Deposited 2007-07-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain O 39–135（97 aa） Chain P 39–135（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å R-free 0.312
2QR0 Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs Deposited 2007-07-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain U 39–135（97 aa） Chain V 39–135（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å R-free 0.312
2VGH HEPARIN-BINDING DOMAIN FROM VASCULAR ENDOTHELIAL GROWTH FACTOR, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-12-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 137–215（79 aa） Fragment：HEPARIN-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；300 K	Resolution not provided
2VPF VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESOLUTION Deposited 1997-07-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109 Chain D 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop	Resolution 1.93 Å R-free 0.272
2VPF VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESOLUTION Deposited 1997-07-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109 Chain B 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop	Resolution 1.93 Å R-free 0.272
2VPF VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESOLUTION Deposited 1997-07-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109 Chain F 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop	Resolution 1.93 Å R-free 0.272
2VPF VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESOLUTION Deposited 1997-07-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109 Chain H 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop	Resolution 1.93 Å R-free 0.272
3BDY Dual specific bH1 Fab in complex with VEGF Deposited 2007-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain V 34–135（102 aa） Fragment：sequence database residues 27-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；For crystallization of the Fab/VEGF (8-109) complex, equal volumes of protein complex solution (10.6 mg/ml protein, 300 mM NaCl, 25 mM Tris-HCl pH 7.5) and crystallization buffer containing 0.15 D, L Malic Acid pH 7.0, 20% PEG3350 were mixed and equilibrated at 19 C. Prior to data collection the crystals were cryo-protected by transfer between drops containing 5%, 10% and 15% Glycerol in artificial mother liquor, followed by flash freeze in liquid nitrogen, VAPOR DIFFUSION, temperature 292K	Resolution 2.60 Å R-free 0.252
3P9W Crystal structure of an engineered human autonomous VH Domain in complex with VEGF Deposited 2010-10-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 35–138（104 aa） Fragment：unp residues 7-110	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10 %(w/v) PEG 4000, 20 %(w/v) Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.233
3P9W Crystal structure of an engineered human autonomous VH Domain in complex with VEGF Deposited 2010-10-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 35–138（104 aa） Fragment：unp residues 7-110	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10 %(w/v) PEG 4000, 20 %(w/v) Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.233
3P9W Crystal structure of an engineered human autonomous VH Domain in complex with VEGF Deposited 2010-10-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 35–138（104 aa） Fragment：unp residues 7-110	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10 %(w/v) PEG 4000, 20 %(w/v) Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.233
3P9W Crystal structure of an engineered human autonomous VH Domain in complex with VEGF Deposited 2010-10-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 35–138（104 aa） Fragment：unp residues 7-110	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10 %(w/v) PEG 4000, 20 %(w/v) Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.233
3QTK The crystal structure of chemically synthesized VEGF-A Deposited 2011-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 34–135（102 aa） Fragment：UNP residues 34-135 Chain D 34–135（102 aa） Fragment：UNP residues 34-135	Not recorded	ACT ACETATE ION × 2 TFA trifluoroacetic acid × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；45% v/v MPD, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.85 Å R-free 0.223
3QTK The crystal structure of chemically synthesized VEGF-A Deposited 2011-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 34–135（102 aa） Fragment：UNP residues 34-135 Chain C 34–135（102 aa） Fragment：UNP residues 34-135	Not recorded	ACT ACETATE ION × 3 TFA trifluoroacetic acid × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；45% v/v MPD, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.85 Å R-free 0.223
3QTK The crystal structure of chemically synthesized VEGF-A Deposited 2011-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 34–135（102 aa） Fragment：UNP residues 34-135 Chain F 34–135（102 aa） Fragment：UNP residues 34-135	Not recorded	ACT ACETATE ION × 3 TFA trifluoroacetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；45% v/v MPD, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.85 Å R-free 0.223
3S1B The Development of Peptide-based Tools for the Analysis of Angiogenesis Deposited 2011-05-14	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 38–133（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1 M NaOAc, 0.02 M CaCl2, MPD 30.0% v/v, pH 6.0, vapor diffusion, hanging drop, temperature 289K	Resolution 2.90 Å R-free 0.251
3S1K The Development of Peptide-based Tools for the Analysis of Angiogenesis Deposited 2011-05-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 34–135（102 aa） Chain W 34–135（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.2 M KI, 0.1 M MES, PEG 4000 25.0% v/v, pH 6.5, vapor diffusion, hanging drop, temperature 289K	Resolution 2.55 Å R-free 0.271
3V2A VEGFR-2/VEGF-A COMPLEX STRUCTURE Deposited 2011-12-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 27–140（114 aa） Fragment：UNP residues 27-140	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M NaCl, 1.6 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.20 Å R-free 0.300
4DEQ Structure of the Neuropilin-1/VEGF-A complex Deposited 2012-01-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 183–232（50 aa） Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain Chain B 183–232（50 aa） Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1.5M Na/K phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.267
4DEQ Structure of the Neuropilin-1/VEGF-A complex Deposited 2012-01-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 183–232（50 aa） Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1.5M Na/K phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.267
4DEQ Structure of the Neuropilin-1/VEGF-A complex Deposited 2012-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 183–232（50 aa） Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1.5M Na/K phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.267
4GLN Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21/n Deposited 2012-08-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 34–135（102 aa） Chain F 34–135（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；292 K；Proteins were dissolved in 0.01 M HEPES, 50 mM NaCl at pH 8.4 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES, 12.5% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.60 Å R-free 0.264
4GLS Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21 Deposited 2012-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 34–135（102 aa） Chain F 34–135（102 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；292 K；Proteins were dissolved in 0.01 M HEPES, 50 mM NaCl at pH 8.4 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES, 12.5% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.60 Å R-free 0.231
4KZN crystal structure of human VEGF-A receptor binding domain Deposited 2013-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 39–135（97 aa） Fragment：receptor binding domain, UNP residues 39-135	Not recorded	PGE TRIETHYLENE GLYCOL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；Li2SO4, PEG200, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.71 Å R-free 0.218
4QAF Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109) Deposited 2014-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 34–135（102 aa） Fragment：UNP residues 34-135 Chain D 34–135（102 aa） Fragment：UNP residues 34-135	Not recorded	OMA 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid × 2 SO4 SULFATE ION × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；1 M sodium chloride, 0.2 M lithium sulfate, 7.5% w/v dextran sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.242
4WPB Vascular endothelial growth factor in complex with alpha/beta-VEGF-1 Deposited 2014-10-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 214–315（102 aa） Chain B 214–315（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M magnesium formate dihydrate, 15% (w/v) PEG3350, 30% (v/v) glycerol	Resolution 3.11 Å R-free 0.298
4ZFF Dual-acting Fab 5A12 in complex with VEGF Deposited 2015-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 217–315（99 aa） Fragment：UNP residues 217-315 Chain D 217–315（99 aa） Fragment：UNP residues 217-315	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris pH 8.0, 2.0 M ammonium sulfate, 0.3 M NDSB-195	Resolution 2.75 Å R-free 0.238
5DN2 Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A Deposited 2015-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 205–232（28 aa） Fragment：VEGF-A165-HBD, UNP residues 205-232	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；289 K；10% PEG20000, 0.1M Bicine, 2% v/v dioxane	Resolution 1.95 Å R-free 0.234
5DN2 Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A Deposited 2015-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 205–232（28 aa） Fragment：VEGF-A165-HBD, UNP residues 205-232	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；289 K；10% PEG20000, 0.1M Bicine, 2% v/v dioxane	Resolution 1.95 Å R-free 0.234
5DN2 Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A Deposited 2015-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 205–232（28 aa） Fragment：VEGF-A165-HBD, UNP residues 205-232	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；289 K；10% PEG20000, 0.1M Bicine, 2% v/v dioxane	Resolution 1.95 Å R-free 0.234
5FV1 Crystal structure of hVEGF in complex with VK domain antibody Deposited 2016-02-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 27–136（110 aa） Fragment：VEGF RESIDUES 27-136 Chain W 27–136（110 aa） Fragment：VEGF RESIDUES 27-136	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；277 K；20% PEG3350, 0.1M BIS TRIS PROPANE PH 8.5, 0.2M NA CITRATE 4C	Resolution 2.70 Å R-free 0.261
5FV2 Crystal structure of hVEGF in complex with VH domain antibody Deposited 2016-02-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 27–136（110 aa） Fragment：VEGF UNP RESIDUES 27-136 Chain W 27–136（110 aa） Fragment：VEGF UNP RESIDUES 27-136	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；0.1M TRIS PH 8.5, 7%PEG6000, 0.2M MGCL2 20C	Resolution 3.45 Å R-free 0.263
5FV2 Crystal structure of hVEGF in complex with VH domain antibody Deposited 2016-02-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 27–136（110 aa） Fragment：VEGF UNP RESIDUES 27-136	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；0.1M TRIS PH 8.5, 7%PEG6000, 0.2M MGCL2 20C	Resolution 3.45 Å R-free 0.263
5HHC Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21/n Deposited 2016-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 214–315（102 aa） Chain B 214–315（102 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；Proteins were dissolved in 0.01 M HEPES at pH 7.0 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES (pH 7.0), 11% (v/v) PEG3350	Resolution 2.10 Å R-free 0.307
5HHD Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21 Deposited 2016-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 214–315（102 aa） Chain B 214–315（102 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；Proteins were dissolved in 0.01 M HEPES at pH 7.0 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES (pH 7.0), 11% (v/v) PEG3350	Resolution 2.10 Å R-free 0.282
5O4E Crystal structure of VEGF in complex with heterodimeric Fcab JanusCT6 Deposited 2017-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 39–134（96 aa） Chain F 39–134（96 aa）	Mutation：E13M Mutation：E13M	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 10 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 CAC CACODYLATE ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M Sodium cacodylate, 40% (v/v) MPD, 5% (w/v) PEG 8000	Resolution 2.15 Å R-free 0.236
5T89 Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6 Deposited 2016-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 27–147（121 aa） Chain W 27–147（121 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；10-14% PEG3000 200 mM calcium chloride 100 mM MES pH 6.5	Resolution 4.00 Å R-free 0.315
6BFT Structure of Bevacizumab Fab mutant in complex with VEGF Deposited 2017-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 216–315（100 aa） Fragment：UNP residues 214-315 Chain G 216–315（100 aa） Fragment：UNP residues 214-315	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM MES, 6.0, 225 mM ammonium sulfate, 13% PEG4000, 10% isopropanol	Resolution 2.55 Å R-free 0.220
6T9D Crystal structure of a bispecific DutaFab in complex with human VEGF121 Deposited 2019-10-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain CCC 27–147（121 aa） Chain DDD 27–147（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；VEGFA-121 from Peprotech, catalogue number 100-20A, was mixed at a 1:1 molar ratio to VEGF monomer. The complex was concentrated to 11 mg/ml. Crystallization involved hanging drop vapour diffusion against 0.1 M MES pH 6.5 and 1.6 M magnesium sulphate. Crystals grew in about 120 days and were frozen in liquid nitrogen with 20 % glycerol as cryoprotectant.	Resolution 2.90 Å R-free 0.280
6V7K Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-109) with one copy of HH4, an alpha/beta-Peptide with Irregular Secondary Structure Deposited 2019-12-08	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 34–135（102 aa） Chain B 34–135（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v PEG 10000	Resolution 2.50 Å R-free 0.278
6Z13 VEGF-A 13:107 crystallized with 3C bicyclic peptide Deposited 2020-05-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 39–133（95 aa） Chain W 39–133（95 aa）	Not recorded	NH2 AMINO GROUP × 1 ACY ACETIC ACID × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；(VEGF)2:2 peptide_3C complex purified on SEC and concentrated at 9.8mg/ml in Tris/HCl 10mM pH 8.5. Mix of 1ul of complex with 1 ul of reservoir : NaOAc/HCl 100mM pH 4.6 / MPD 36% (v/v) / CaCl2 20mM	Resolution 1.80 Å R-free 0.247
6Z3F VEGF-A 13:107 crystallized with 2C bicyclic peptide Deposited 2020-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 39–133（95 aa） Chain W 39–133（95 aa）	Not recorded	NH2 AMINO GROUP × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 ACY ACETIC ACID × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；(VEGF)2:2 PEPTIDE_3C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 / MPD 35% (V/V) / (NH4)2PO4 150MM	Resolution 2.10 Å R-free 0.265
6ZBR VEGF-A 13:107 crystallized with 4C bicyclic peptide Deposited 2020-06-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 39–133（95 aa） Chain W 39–133（95 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；(VEGF)2:2 PEPTIDE_4C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 / MPD 35% (V/V) / (NH4)2PO4 150MM	Resolution 1.60 Å R-free 0.241
6ZCD VEGF-A 13:107 crystallized with 1C bicyclic peptide Deposited 2020-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 39–133（95 aa） Chain W 39–133（95 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；(VEGF)2:2 PEPTIDE_1C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 13.5MG/ML IN TRIS/HCL 10MM PH 8.5. MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 / MPD 35% (V/V) / (NH4)2PO4 150MM	Resolution 1.80 Å R-free 0.242
6ZFL High resolution structure of VEGF-A 12:107 crystallized in tetragonal form Deposited 2020-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain V 219–313（95 aa） Chain W 219–313（95 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；(VEGF)2:2 PEPTIDE_2C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. (SEE ID 6Z3F) mix 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : TRIS/HCL 100MM PH 8.5 / MPD 42% (V/V) / (NH4)2PO4 200MM	Resolution 1.60 Å R-free 0.186
7LL8 D-Protein RFX-V1 Bound to the VEGFR1 Domain 2 Site on VEGF-A Deposited 2021-02-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 214–315（102 aa） Chain B 214–315（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.2 K；calcium chloride, Tris, PEG4000	Resolution 2.31 Å R-free 0.314
7LL9 D-Protein RFX-V2 Bound to the VEGFR1 Domain 3 Site on VEGF-A Deposited 2021-02-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 214–315（102 aa） Chain B 214–315（102 aa） Chain E 214–315（102 aa） Chain F 214–315（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.2 K；magnesium chloride, Bis-Tris, PEG3350	Resolution 2.90 Å R-free 0.315
8UWZ The structure of Raamsizumab in complex with VEGF121 Deposited 2023-11-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 27–147（121 aa） Chain F 27–147（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；298 K；0.2 M Sodium Phosphate mono basic, 30% PEG600	Resolution 3.50 Å R-free 0.298
9JU1 Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A Deposited 2024-10-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 214–315（102 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；pH 8；277 K；0.1M Tris-HCl pH 8.0, 0.2M NaCl, 2.5M Ammonium Sulfate, 0.04% NaN3	Resolution 1.45 Å R-free 0.245
9KKU Helix-loop-helix peptide (M49) in complex with VEGF-A Deposited 2024-11-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 214–315（102 aa） Chain B 214–315（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；pH 5.6；293 K；0.2M NH4-AcOH pH 5.6, 14% PEG 3350, 20% 2-Propanol, 0.2M CaCl2,, 0.4M NaCl, 0.04% NaN3	Resolution 1.46 Å R-free 0.250

50 other PDB entries and 72 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VEGFA_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–102； UniProt 34–135 Author chain B； PDBConstruct 1–102； UniProt 34–135

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6d3o
Deposition date deposition_date	2018-04-16
Structure title title	Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-109) with HH4, an alpha/beta-Peptide with Irregular Secondary Structure
Keywords keywords	alpha/beta-peptide, VEGF, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.15 Å
Radius of gyration Rg (electron density) rg_electron	20.57 Å
Forward intensity I(0) i0	11351600.00
Molecular weight molecular_weight	24729.0 kDa
Excluded volume excluded_volume	30651 Å³
Envelope volume envelope_volume	38852 Å³
Hydration-shell volume shell_volume	16281 Å³
Envelope diameter envelope_diameter	72.9 Å
Shell Rg shell_rg	26.38 Å
Envelope Rg envelope_rg	20.77 Å
Shape Rg shape_rg	20.64 Å
Total Rg total_rg	21.22 Å
Total atoms total_atoms	1720
Residues n_residues	211
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	74.2 Å
Rg (real space) rg_real	21.23 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	1.1350e+07
I(0) uncertainty (real space) i0_real_error	1.6730e+05
Rg (reciprocal space) rg_reciprocal	21.22 Å
I(0) (reciprocal space) i0_reciprocal	11350000.0000
Solution quality estimate total_estimate	0.8652
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.437
Kurtosis Kurtosis kurtosis	-0.219
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1315000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.860; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Vascular endothelial growth factor A
Molecular weight formula_weight	11862.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1722

GQNHHEVVKFMDVYQQSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGEHIGEMSFLQHNKCECRPKAD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Vascular endothelial growth factor A
Molecular weight formula_weight	11948.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	HH4 alpha/beta-Peptide
Molecular weight formula_weight	1992.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

NCDIHVLWEWECFXR

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6d3oA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	6d3oB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

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8. Citations (1)

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Unit-cell length a length_a	101.649 Å
Unit-cell length b length_b	101.649 Å
Unit-cell length c length_c	59.988 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	33.290 Å
R factor r_factor	0.2192
R_work r_work	0.2166
R_free r_free	0.2789

fit	/app/data/saxs_computation/d3/6d3o/6d3o.fit
pddf	/app/data/pr_computation/d3/6d3o/6d3o.pr.out
profile	/app/data/saxs_computation/d3/6d3o/6d3o.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Vascular endothelial growth factor A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)