2qr0

Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs

Method: X-RAY DIFFRACTION D_max: 230.6 Å Quality: EXCELLENT

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

Vascular endothelial growth factor A

OrganismNot specified

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain C； UniProt 39–135 Chain D； UniProt 39–135	Not recorded	Fab-Fragment Light Chain × 2 Fab-Fragment Heavy Chain × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.50 Å R-free 0.312
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain I； UniProt 39–135 Chain J； UniProt 39–135	Not recorded	Fab-Fragment Light Chain × 2 Fab-Fragment Heavy Chain × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.50 Å R-free 0.312
3	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain O； UniProt 39–135 Chain P； UniProt 39–135	Not recorded	Fab-Fragment Light Chain × 2 Fab-Fragment Heavy Chain × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.50 Å R-free 0.312
4	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain U； UniProt 39–135 Chain V； UniProt 39–135	Not recorded	Fab-Fragment Light Chain × 2 Fab-Fragment Heavy Chain × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.50 Å R-free 0.312

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 2QR0	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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 oligomeric state 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
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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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
6D3O Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-109) with HH4, an alpha/beta-Peptide with Irregular Secondary Structure Deposited 2018-04-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 34–135（102 aa） Fragment：residues 34-135 Chain B 34–135（102 aa） Fragment：residues 34-135	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 3.10 Å R-free 0.279
6T9D Crystal structure of a bispecific DutaFab in complex with human VEGF121 Deposited 2019-10-28	Different construct 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 experimental conditions 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 69 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VEGFA_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–97； UniProt 39–135 Author chain D； PDBConstruct 1–97； UniProt 39–135 Author chain I； PDBConstruct 1–97； UniProt 39–135 Author chain J； PDBConstruct 1–97； UniProt 39–135 Author chain O； PDBConstruct 1–97； UniProt 39–135 Author chain P； PDBConstruct 1–97； UniProt 39–135 Author chain U； PDBConstruct 1–97； UniProt 39–135 Author chain V； PDBConstruct 1–97； UniProt 39–135

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.

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P(r) Distance Distribution P(r) Distribution

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2qr0
Deposition date deposition_date	2007-07-27
Structure title title	Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs
Keywords keywords	VEGF; Antibody Recognition; Specificity; Phage Display, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	85.53 Å
Radius of gyration Rg (electron density) rg_electron	88.28 Å
Forward intensity I(0) i0	3058760000.00
Molecular weight molecular_weight	460490.0 kDa
Excluded volume excluded_volume	573080 Å³
Envelope volume envelope_volume	952860 Å³
Hydration-shell volume shell_volume	108640 Å³
Envelope diameter envelope_diameter	364.7 Å
Shell Rg shell_rg	62.69 Å
Envelope Rg envelope_rg	88.32 Å
Shape Rg shape_rg	88.27 Å
Total Rg total_rg	87.89 Å
Total atoms total_atoms	32356
Residues n_residues	4144
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

▼

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

Maximum dimension Dmax dmax	230.6 Å
Rg (real space) rg_real	77.77 Å
Rg uncertainty (real space) rg_real_error	1.18 Å
I(0) (real space) i0_real	2.9090e+09
I(0) uncertainty (real space) i0_real_error	6.2870e+07
Rg (reciprocal space) rg_reciprocal	79.12 Å
I(0) (reciprocal space) i0_reciprocal	3004000000.0000
Solution quality estimate total_estimate	0.9150
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	76.9 Å
Skewness Skewness skewness	0.465
Kurtosis Kurtosis kurtosis	-0.528
Angular range angular_range	— – 0.0900 Å⁻¹
Current regularization parameter α current_alpha	0.5292
Highest regularization parameter α highest_alpha	110400000.0000
Real-space data points n_real_points	19
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.004; Oscil: 0.968; Stabil: 0.982; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.061

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Fab-Fragment Light Chain
Molecular weight formula_weight	23497.0 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,G,K,M,Q,S,W
Atom count atom_count	32356

DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYSYYYYPFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Entity 2 Entity 2 polymer

Description description	Fab-Fragment Heavy Chain
Molecular weight formula_weight	23362.0 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,H,L,N,R,T,X

EVQLVESGGGLVQPGGSLRLSCAASGFNFSSSSIHWVRQAPGKGLEWVAYIYPSYSYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYYGTGAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Entity 3 Entity 3 polymer

Description description	Vascular endothelial growth factor A
Molecular weight formula_weight	11373.1 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,I,J,O,P,U,V

EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

▼

7. Fold Classification (SCOP + CATH) 80 domains

SCOP 2.08 (40 domains)

Domain ID domain_id	d2qr0a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0a2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0b1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0b2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0c1
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

Domain ID domain_id	d2qr0d1
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

Domain ID domain_id	d2qr0e1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0e2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0f1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0f2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0g1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0g2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0h2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0i1
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

Domain ID domain_id	d2qr0j1
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

Domain ID domain_id	d2qr0k1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0k2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0m1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0m2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0n1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0n2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0o1
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

Domain ID domain_id	d2qr0p1
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

Domain ID domain_id	d2qr0q1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0q2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0r1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0r2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0s1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0s2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0t1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0t2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0u1
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

Domain ID domain_id	d2qr0v1
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.1 — Platelet-derived growth factor-like

Domain ID domain_id	d2qr0w1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0w2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2qr0x1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2qr0x2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (40 domains)

Domain ID domain_id	2qr0A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0C00
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	2qr0D00
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	2qr0E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0F01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0F02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0G02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0I00
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	2qr0J00
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	2qr0K01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0K02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0M01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0M02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0N01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0N02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0O00
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	2qr0P00
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	2qr0Q01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0Q02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0R01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0R02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0S01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0S02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0T01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0T02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0U00
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	2qr0V00
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	2qr0W01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0W02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0X01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qr0X02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	154.453 Å
Unit-cell length b length_b	90.218 Å
Unit-cell length c length_c	205.558 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2920
R_work r_work	0.2910
R_free r_free	0.3120

Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 80 domains

SCOP 2.08 (40 domains)

CATH v4.4 (40 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/qr/2qr0/2qr0.fit
pddf	/app/data/pr_computation/qr/2qr0/2qr0.pr.out
profile	/app/data/saxs_computation/qr/2qr0/2qr0.dat