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1kmx

Heparin-binding Domain from Vascular Endothelial Growth Factor

Method: SOLUTION NMR Dmax: 39.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

vascular endothelial growth factor

Homo sapiens

UniProt P15692

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 137–191 Fragment：heparin-binding domain No other associated polymer 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

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 1KMX 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental conditions 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
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 method 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 method 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 method 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 method 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 method 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different experimental method 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 method 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 mutation/modification Different oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 experimental conditions 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 experimental conditions 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 mutation/modification 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 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 oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification 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 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 mutation/modification 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 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 oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 method 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 mutation/modification Different oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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
Chains and sequence ranges Author chain A； PDBConstruct 1–55； UniProt 137–191

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

SAXS profile for 1kmx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1kmx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1kmx
Deposition date deposition_date2001-12-17
Structure title titleHeparin-binding Domain from Vascular Endothelial Growth Factor
Keywords keywordsheparin-binding, angiogenesis, growth factor, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.98 Å
Radius of gyration Rg (electron density) rg_electron15.21 Å
Forward intensity I(0) i0324415000.00
Molecular weight molecular_weight129110.0 kDa
Excluded volume excluded_volume153510 ų
Envelope volume envelope_volume28335 ų
Hydration-shell volume shell_volume13266 ų
Envelope diameter envelope_diameter70.9 Å
Shell Rg shell_rg24.53 Å
Envelope Rg envelope_rg20.76 Å
Shape Rg shape_rg15.25 Å
Total Rg total_rg15.37 Å
Total atoms total_atoms17620
Residues n_residues1100
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax39.7 Å
Rg (real space) rg_real13.77 Å
Rg uncertainty (real space) rg_real_error0.09 Å
I(0) (real space) i0_real3.0840e+08
I(0) uncertainty (real space) i0_real_error2.5570e+06
Rg (reciprocal space) rg_reciprocal15.32 Å
I(0) (reciprocal space) i0_reciprocal324400000.0000
Solution quality estimate total_estimate0.6754
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary12.6 Å
Skewness Skewness skewness0.357
Kurtosis Kurtosis kurtosis-0.616
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha2.9260
Highest regularization parameter α highest_alpha91750.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.011; Oscil: 0.990; Stabil: 0.990; Sysdev: 0.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1kmxa_
Class classg — Small proteins
Fold Fold foldg.25 — Heparin-binding domain from vascular endothelial growth factor
Superfamily Superfamily superfamilyg.25.1 — Heparin-binding domain from vascular endothelial growth factor
Family Family familyg.25.1.1 — Heparin-binding domain from vascular endothelial growth factor

CATH v4.4 (1 domains)

Domain ID domain_id1kmxA00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology160 — Vascular Endothelial Growth Factor-165, Heparin-binding Domain
Homologous superfamily homologous superfamily10 — Vascular endothelial growth factor, heparin-binding domain
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8. Citations (2)

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9. Files and Curves (10)