Vascular endothelial growth factor A
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain V； UniProt 38–133 | Not recorded | mini-Z × 2 | 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 |
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 3S1B | 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 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 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 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 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 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 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain V
34–135（102 aa）
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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 |
| 3S1K The Development of Peptide-based Tools for the Analysis of Angiogenesis Deposited 2011-05-15 | Different construct Different mutation/modification 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 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 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 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 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 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 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 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
214–315（102 aa）
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
27–147（121 aa）
Chain W
27–147（121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；293 K；10-14% PEG3000
200 mM calcium chloride
100 mM MES pH 6.5
|
Resolution 4.00 Å R-free 0.315 |
| 6BFT Structure of Bevacizumab Fab mutant in complex with VEGF Deposited 2017-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
216–315（100 aa）
Fragment：UNP residues 214-315
Chain G
216–315（100 aa）
Fragment：UNP residues 214-315
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；100 mM MES, 6.0, 225 mM ammonium sulfate, 13% PEG4000, 10% isopropanol
|
Resolution 2.55 Å R-free 0.220 |
| 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 mutation/modification 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 V； PDBConstruct 1–96； UniProt 38–133 |
