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4deq

Structure of the Neuropilin-1/VEGF-A complex

Method: X-RAY DIFFRACTION Dmax: 87.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neuropilin-1, Vascular endothelial growth factor A

Homo sapiens

UniProt O14786

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 274–429 Chain B； UniProt 274–429 Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain 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
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 274–429 Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain No other associated polymer 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
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 274–429 Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain 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

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 4DEQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1KEX Crystal Structure of the b1 Domain of Human Neuropilin-1 Deposited 2001-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa） Fragment：b1 domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；PEG 8000, MES, zinc acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 1.90 Å R-free 0.266
2QQI Crystal Structure of the b1b2 Domains from Human Neuropilin-1 Deposited 2007-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–586（314 aa） Fragment：F5/8 type C 1 and C 2 domains
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20% PEG 3350, 0.2 M Sodium Fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.80 Å R-free 0.201
2QQM Crystal Structure of the a2b1b2 Domains from Human Neuropilin-1 Deposited 2007-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric
Chain A 141–586（446 aa） Fragment：CUB 2, F5/8 type C 1, and F5/8 type C 2 domains
Not recorded CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；0.1 M MES, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 2.00 Å R-free 0.243
2QQN Neuropilin-1 b1 Domain in Complex with a VEGF-Blocking Fab Deposited 2007-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 273–427（155 aa） Fragment：F5/8 type C 1 domain
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；25% PEG 1500, 4% tert-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 2.20 Å R-free 0.207
3I97 B1 domain of human Neuropilin-1 bound with small molecule EG00229 Deposited 2009-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa） Fragment：domain B1, F5/8 type C 1
Not recorded 8DR (S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；293.15 K；100 mM MES (pH 6.0), 10% PEG 8K and 200 mM Zn(AcO, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.90 Å R-free 0.282
3I97 B1 domain of human Neuropilin-1 bound with small molecule EG00229 Deposited 2009-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 273–427（155 aa） Fragment：domain B1, F5/8 type C 1
Not recorded 8DR (S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；293.15 K；100 mM MES (pH 6.0), 10% PEG 8K and 200 mM Zn(AcO, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.90 Å R-free 0.282
4RN5 B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site Deposited 2014-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa） Fragment：B1 domain (UNP residues 273-427)
Not recorded ACT ACETATE ION × 1 ZN ZINC ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；100mM MES, 200mM Zinc Acetate, 10% PEG 8000, pH 6.0, VAPOR DIFFUSION, temperature 293K
Resolution 1.73 Å R-free 0.201
5C7G Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule Deposited 2015-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa） Fragment：B1 DOMAIN, UNP residues 273-427
Not recorded BCN BICINE × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG550 mme 5%, PEG 20 000, 60mM MgCl2, Na-Bicine 100 mM, pH 8.5
Resolution 1.45 Å R-free 0.172
5IJR X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand. Deposited 2016-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa） Fragment：b1 domain, UNP residues 273-427
Not recorded HRG L-HOMOARGININE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；28% w/v PEG3350, 0.2 M AmCl
Resolution 1.52 Å R-free 0.213
5IJR X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand. Deposited 2016-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 273–427（155 aa） Fragment：b1 domain, UNP residues 273-427
Not recorded DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；28% w/v PEG3350, 0.2 M AmCl
Resolution 1.52 Å R-free 0.213
5IYY X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand. Deposited 2016-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa）
Not recorded R40 N~2~-[(benzyloxy)carbonyl]-L-arginine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；30% w/v PEG3350, 0.2 M AmCl
Resolution 1.60 Å R-free 0.187
5IYY X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand. Deposited 2016-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 273–427（155 aa）
Not recorded R40 N~2~-[(benzyloxy)carbonyl]-L-arginine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；30% w/v PEG3350, 0.2 M AmCl
Resolution 1.60 Å R-free 0.187
5J1X X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand. Deposited 2016-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa）
Not recorded AR5 N~2~-(tert-butoxycarbonyl)-L-arginine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；18% w/v PEG3350, 0.2M NH4Cl
Resolution 2.10 Å R-free 0.223
5J1X X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand. Deposited 2016-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 273–427（155 aa）
Not recorded AR5 N~2~-(tert-butoxycarbonyl)-L-arginine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；18% w/v PEG3350, 0.2M NH4Cl
Resolution 2.10 Å R-free 0.223
5J1X X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand. Deposited 2016-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 273–427（155 aa）
Not recorded AR5 N~2~-(tert-butoxycarbonyl)-L-arginine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；18% w/v PEG3350, 0.2M NH4Cl
Resolution 2.10 Å R-free 0.223
5J1X X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand. Deposited 2016-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 273–427（155 aa）
Not recorded AR5 N~2~-(tert-butoxycarbonyl)-L-arginine × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；18% w/v PEG3350, 0.2M NH4Cl
Resolution 2.10 Å R-free 0.223
5JGI X-ray structure of neuropilin-1 b1 domain complexed with M45 compound Deposited 2016-04-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；20% PEG3350+0.2 M NH4Cl
Resolution 1.38 Å R-free 0.169
5JGI X-ray structure of neuropilin-1 b1 domain complexed with M45 compound Deposited 2016-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 273–427（155 aa）
Not recorded AAG N-ALPHA-L-ACETYL-ARGININE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；20% PEG3350+0.2 M NH4Cl
Resolution 1.38 Å R-free 0.169
5JGQ X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand. Deposited 2016-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；18%PEG3350+0.2M NH4Cl
Resolution 1.60 Å R-free 0.193
5JGQ X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand. Deposited 2016-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 273–427（155 aa）
Not recorded 6JY N~2~-(benzenecarbonyl)-L-arginine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；18%PEG3350+0.2M NH4Cl
Resolution 1.60 Å R-free 0.193
5JHK X-ray structure of neuropilin-1 b1 domain complexed with Arg-6 ligand. Deposited 2016-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa）
Not recorded 6K8 N-(benzenecarbonyl)glycyl-L-arginine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；30%PEG3350+0,2M NH4Cl
Resolution 1.80 Å R-free 0.215
5JHK X-ray structure of neuropilin-1 b1 domain complexed with Arg-6 ligand. Deposited 2016-04-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 273–427（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；30%PEG3350+0,2M NH4Cl
Resolution 1.80 Å R-free 0.215
5L73 MAM domain of human neuropilin-1 Deposited 2016-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 628–813（186 aa） Fragment：UNP residues 628-813
Chain B 628–813（186 aa） Fragment：UNP residues 628-813
Not recorded CA CALCIUM ION × 4 BCN BICINE × 2 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；0.06 M MgCl2 0.06 M CaCl2 0.1 M Tris (base), 0.1 M BICINE pH 8.0 12.5 % MPD 12.5 % PEG 1000 12.5 % w/v PEG 3350.
Resolution 2.24 Å R-free 0.228
6FMC Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure Deposited 2018-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa）
Not recorded DUE (2~{S})-2-[[3-[[5-[4-(aminomethyl)phenyl]-1-benzofuran-7-yl]sulfonylamino]thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；16 % w/v PEG3350 and 200 mM ammonium chloride
Resolution 0.90 Å R-free 0.132
6FMF Neuropilin-1 b1 domain in complex with EG01377; 2.8 Angstrom structure Deposited 2018-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa）
Not recorded DUE (2~{S})-2-[[3-[[5-[4-(aminomethyl)phenyl]-1-benzofuran-7-yl]sulfonylamino]thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid × 1 TFA trifluoroacetic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；16 % w/v PEG3350 and 200 mM ammonium chloride
Resolution 2.81 Å R-free 0.292
6TKK Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide Deposited 2019-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 273–427（155 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；16 % w/v PEG3350 and 200 mM ammonium chloride
Resolution 1.06 Å R-free 0.149
7JJC Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide Deposited 2020-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 273–427（155 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M Sodium Citrate pH 5, 20% PEG 6K
Resolution 2.36 Å R-free 0.250
7JJC Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide Deposited 2020-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 273–427（155 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M Sodium Citrate pH 5, 20% PEG 6K
Resolution 2.36 Å R-free 0.250
7JJC Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide Deposited 2020-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 273–427（155 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M Sodium Citrate pH 5, 20% PEG 6K
Resolution 2.36 Å R-free 0.250
7JJC Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide Deposited 2020-07-25 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 D 273–427（155 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M Sodium Citrate pH 5, 20% PEG 6K
Resolution 2.36 Å R-free 0.250
7O1N Crystal Structure of Human Neuropilin-1 b1 Domain mutant - Y297A Deposited 2021-03-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 273–427（155 aa）
Mutation：Y297A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Precipitant of 20% PEG4000, 0.1M Tris (pH 8.5), 0.2M Lithium Sulfate. Protein concentration used is 10 mg/mL, mixed 1:1 with precipitant for hanging drop over reservoir of 1 mL.
Resolution 1.56 Å R-free 0.209
7P5U Neuropilin-b1 in a complex with a VEGFB-derived peptide Deposited 2021-07-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain AAA 273–427（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；10 to 30% PEG 3350 + 0.2 M ammonium chloride
Resolution 1.60 Å R-free 0.214
7P5U Neuropilin-b1 in a complex with a VEGFB-derived peptide Deposited 2021-07-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain BBB 273–427（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；10 to 30% PEG 3350 + 0.2 M ammonium chloride
Resolution 1.60 Å R-free 0.214
8C5G Structure of human Neuropilin-1 b1b2 domains in complex with Chlorotoxin (Leiurus quinquestriatus) Deposited 2023-01-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 271–586（316 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.04M Potassium phosphate monobasic 16 % w/v PEG 8000 20 % v/v Glycerol (JCSG Plus: D12)
Resolution 2.70 Å R-free 0.314
8C5G Structure of human Neuropilin-1 b1b2 domains in complex with Chlorotoxin (Leiurus quinquestriatus) Deposited 2023-01-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 271–586（316 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.04M Potassium phosphate monobasic 16 % w/v PEG 8000 20 % v/v Glycerol (JCSG Plus: D12)
Resolution 2.70 Å R-free 0.314
8PFE Crystal Structure of an Hexavariant of the b1 Domain of Human Neuropilin-1 in Complex with the KDKPPR Peptide Deposited 2023-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 273–427（155 aa）
Mutation：E277K, E285K, D289K, E367K, K373E, K397E ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.3 ul protein + 0.3 ul crystallization solution (0.2 M ammonium citrate, 0.1 M bis-tris pH 5.5 and 25% w/v PEG 3350, from JCSGplus); soaked in their mother liquor supplemented with 20% glycerol
Resolution 1.35 Å R-free 0.210
8PFE Crystal Structure of an Hexavariant of the b1 Domain of Human Neuropilin-1 in Complex with the KDKPPR Peptide Deposited 2023-06-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 273–427（155 aa）
Mutation：E277K, E285K, D289K, E367K, K373E, K397E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.3 ul protein + 0.3 ul crystallization solution (0.2 M ammonium citrate, 0.1 M bis-tris pH 5.5 and 25% w/v PEG 3350, from JCSGplus); soaked in their mother liquor supplemented with 20% glycerol
Resolution 1.35 Å R-free 0.210
9EOU Crystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a peptide. Deposited 2024-03-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 273–586（314 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M sodium malonate pH 6.0, 9% w/v PEG 3350
Resolution 1.55 Å R-free 0.202
9F6B Human neuropilin-1 in a complex with a quinoline based antagonists Deposited 2024-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 273–427（155 aa）
Chain B 273–427（155 aa）
Not recorded A1IAT (2~{S})-2-[[3-[[6-[3-(aminomethyl)phenyl]quinolin-8-yl]sulfonylamino]thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M Ammonium Chloride, 14% PEG3350
Resolution 1.57 Å R-free 0.239

24 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NRP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–160； UniProt 274–429 Author chain B； PDBConstruct 5–160； UniProt 274–429

Neuropilin-1, Vascular endothelial growth factor A

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 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 183–232 Chain B； UniProt 183–232 Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain 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
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 183–232 Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain No other associated polymer 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
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 183–232 Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain 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

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 4DEQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BJ1 VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY Deposited 1998-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain V 214–315（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Chain W 214–315（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 2.40 Å R-free 0.266
1CZ8 VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH AN AFFINITY MATURED ANTIBODY Deposited 1999-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain V 40–133（94 aa） Fragment：RECEPTOR BINDING FRAGMENT
Chain W 40–133（94 aa） Fragment：RECEPTOR BINDING FRAGMENT
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 4000, ISOPROPANOL, AMMONIUM SULFATE, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.267
1FLT VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1997-11-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 38–135（98 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Chain W 38–135（98 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 1.70 Å R-free 0.261
1FLT VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1997-11-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain V 38–135（98 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Chain W 38–135（98 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 1.70 Å R-free 0.261
1KAT Solution Structure of a Phage-Derived Peptide Antagonist in Complex with Vascular Endothelial Growth Factor Deposited 2001-11-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 37–135（99 aa） Fragment：Receptor Binding Domain
Chain W 37–135（99 aa） Fragment：Receptor Binding Domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 50mM sodium chloride, 20 sodium phosphate；Pressure 1
NMR measurement conditions pH 7；318 K；Ionic strength (raw mmCIF value) 50mM sodium chloride, 20 sodium phosphate；Pressure 1
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50mM sodium chloride, 20 sodium phosphate；Pressure 1
NMR sample composition 0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide | 90% H2O/10% D2O
NMR sample composition 0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide | 100% D2O
NMR sample composition 1.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide | 90% H2O/10% D2O
NMR sample composition 1.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide | 100% D2O
NMR sample composition 0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide, 15mg/ml pf1 phage | 90% H2O/10% D2O
NMR sample composition 1.0mM U-13C/15N labeled VEGF Dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide, 15mg/ml pf1 phage | 90% H2O/10% D2O
Resolution not provided
1KMX Heparin-binding Domain from Vascular Endothelial Growth Factor Deposited 2001-12-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 137–191（55 aa） Fragment：heparin-binding domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 25 mM sodium acetate; 50 mM sodium chloride；Pressure ambient
NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 25 mM sodium acetate; 50 mM sodium chloride；Pressure ambient
NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 25 mM sodium acetate; 50 mM sodium chloride；Pressure ambient
NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 25 mM sodium acetate; 50 mM sodium chloride；Pressure ambient
NMR sample composition 2.0 mM VEGF heparin-binding domain; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide | 90% H2O/10% D2O
NMR sample composition 2.0 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide | 90% H2O/10% D2O
NMR sample composition 2.0 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide | 99.9% D2O
NMR sample composition 0.6 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride; 0.02% sodium azide | 4:1:0.2 ditridecanoyl-phosphatidylcholine/dihexanoyl-phosphatidylcholine/cetyltrimethylammonium bromide, 5% w/v total lipid in 90% H2O, 10% D2O
Resolution not provided
1MJV DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A (C51A and C60A) Deposited 2002-08-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 40–134（95 aa） Fragment：Residues 40-134, Sequence Database
Chain B 40–134（95 aa） Fragment：Residues 40-134, Sequence Database
Mutation：C51A,C60A Mutation：C51A,C60A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；Na-Citrate, isopropanol, PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.248
1MKG DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A (C57A and C102A) Deposited 2002-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 40–134（95 aa） Fragment：Residues 40-134, sequence database
Chain B 40–134（95 aa） Fragment：Residues 40-134, sequence database
Mutation：C57A,C102A Mutation：C57A,C102A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Na-formate 2.0 M, Na-acetate 0.1 M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.288
1MKG DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A (C57A and C102A) Deposited 2002-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 40–134（95 aa） Fragment：Residues 40-134, sequence database
Chain D 40–134（95 aa） Fragment：Residues 40-134, sequence database
Mutation：C57A,C102A Mutation：C57A,C102A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Na-formate 2.0 M, Na-acetate 0.1 M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.288
1MKG DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A (C57A and C102A) Deposited 2002-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 40–134（95 aa） Fragment：Residues 40-134, sequence database
Chain B 40–134（95 aa） Fragment：Residues 40-134, sequence database
Chain C 40–134（95 aa） Fragment：Residues 40-134, sequence database
Chain D 40–134（95 aa） Fragment：Residues 40-134, sequence database
Mutation：C57A,C102A Mutation：C57A,C102A Mutation：C57A,C102A Mutation：C57A,C102A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Na-formate 2.0 M, Na-acetate 0.1 M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.288
1MKK Disulfide deficient mutant of vascular endothelial growth factor A (C61A and C104A) Deposited 2002-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 40–134（95 aa） Fragment：Residues 40-134, sequence database
Chain B 40–134（95 aa） Fragment：Residues 40-134, sequence database
Mutation：C61A,C104A Mutation：C61A,C104A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；isopropanol, PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.32 Å R-free 0.195
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Chain W 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.284
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Chain S 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.284
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Chain S 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Chain V 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Chain W 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.284
1TZH Crystal Structure of the Fab YADS1 Complexed with h-VEGF Deposited 2004-07-09 Different construct Different 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Chain B 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 2.50 Å R-free 0.297
1VPF STRUCTURE OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR Deposited 1997-04-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Chain D 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 2.50 Å R-free 0.297
1VPP COMPLEX BETWEEN VEGF AND A RECEPTOR BLOCKING PEPTIDE Deposited 1998-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Chain W 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 1.90 Å R-free 0.270
2QR0 Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs Deposited 2007-07-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 39–135（97 aa）
Chain D 39–135（97 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å R-free 0.312
2QR0 Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs Deposited 2007-07-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 39–135（97 aa）
Chain J 39–135（97 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å R-free 0.312
2QR0 Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs Deposited 2007-07-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain O 39–135（97 aa）
Chain P 39–135（97 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å R-free 0.312
2QR0 Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs Deposited 2007-07-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain U 39–135（97 aa）
Chain V 39–135（97 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å R-free 0.312
2VGH HEPARIN-BINDING DOMAIN FROM VASCULAR ENDOTHELIAL GROWTH FACTOR, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-12-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 137–215（79 aa） Fragment：HEPARIN-BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；300 K
Resolution not provided
2VPF VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESOLUTION Deposited 1997-07-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Chain D 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop
Resolution 1.93 Å R-free 0.272
2VPF VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESOLUTION Deposited 1997-07-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Chain B 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop
Resolution 1.93 Å R-free 0.272
2VPF VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESOLUTION Deposited 1997-07-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Chain F 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop
Resolution 1.93 Å R-free 0.272
2VPF VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS RESOLUTION Deposited 1997-07-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Chain H 34–135（102 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop
Resolution 1.93 Å R-free 0.272
3BDY Dual specific bH1 Fab in complex with VEGF Deposited 2007-11-15 Different construct Different 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 34–135（102 aa） Fragment：UNP residues 34-135
Chain D 34–135（102 aa） Fragment：UNP residues 34-135
Not recorded ACT ACETATE ION × 2 TFA trifluoroacetic acid × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；45% v/v MPD, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.85 Å R-free 0.223
3QTK The crystal structure of chemically synthesized VEGF-A Deposited 2011-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 34–135（102 aa） Fragment：UNP residues 34-135
Chain C 34–135（102 aa） Fragment：UNP residues 34-135
Not recorded ACT ACETATE ION × 3 TFA trifluoroacetic acid × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；45% v/v MPD, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.85 Å R-free 0.223
3QTK The crystal structure of chemically synthesized VEGF-A Deposited 2011-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 34–135（102 aa） Fragment：UNP residues 34-135
Chain F 34–135（102 aa） Fragment：UNP residues 34-135
Not recorded ACT ACETATE ION × 3 TFA trifluoroacetic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；45% v/v MPD, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.85 Å R-free 0.223
3S1B The Development of Peptide-based Tools for the Analysis of Angiogenesis Deposited 2011-05-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 38–133（96 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1 M NaOAc, 0.02 M CaCl2, MPD 30.0% v/v, pH 6.0, vapor diffusion, hanging drop, temperature 289K
Resolution 2.90 Å R-free 0.251
3S1K The Development of Peptide-based Tools for the Analysis of Angiogenesis Deposited 2011-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 34–135（102 aa）
Chain W 34–135（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.2 M KI, 0.1 M MES, PEG 4000 25.0% v/v, pH 6.5, vapor diffusion, hanging drop, temperature 289K
Resolution 2.55 Å R-free 0.271
3V2A VEGFR-2/VEGF-A COMPLEX STRUCTURE Deposited 2011-12-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 27–140（114 aa） Fragment：UNP residues 27-140
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M NaCl, 1.6 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.20 Å R-free 0.300
4GLN Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21/n Deposited 2012-08-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 34–135（102 aa）
Chain F 34–135（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；292 K；Proteins were dissolved in 0.01 M HEPES, 50 mM NaCl at pH 8.4 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES, 12.5% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.60 Å R-free 0.264
4GLS Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21 Deposited 2012-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 34–135（102 aa）
Chain F 34–135（102 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；292 K；Proteins were dissolved in 0.01 M HEPES, 50 mM NaCl at pH 8.4 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES, 12.5% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.60 Å R-free 0.231
4KZN crystal structure of human VEGF-A receptor binding domain Deposited 2013-05-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 39–135（97 aa） Fragment：receptor binding domain, UNP residues 39-135
Not recorded PGE TRIETHYLENE GLYCOL × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；Li2SO4, PEG200, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.71 Å R-free 0.218
4QAF Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109) Deposited 2014-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 34–135（102 aa） Fragment：UNP residues 34-135
Chain D 34–135（102 aa） Fragment：UNP residues 34-135
Not recorded OMA 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid × 2 SO4 SULFATE ION × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；1 M sodium chloride, 0.2 M lithium sulfate, 7.5% w/v dextran sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.242
4WPB Vascular endothelial growth factor in complex with alpha/beta-VEGF-1 Deposited 2014-10-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 214–315（102 aa）
Chain B 214–315（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M magnesium formate dihydrate, 15% (w/v) PEG3350, 30% (v/v) glycerol
Resolution 3.11 Å R-free 0.298
4ZFF Dual-acting Fab 5A12 in complex with VEGF Deposited 2015-04-21 Different construct Different 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 27–136（110 aa） Fragment：VEGF RESIDUES 27-136
Chain W 27–136（110 aa） Fragment：VEGF RESIDUES 27-136
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；277 K；20% PEG3350, 0.1M BIS TRIS PROPANE PH 8.5, 0.2M NA CITRATE 4C
Resolution 2.70 Å R-free 0.261
5FV2 Crystal structure of hVEGF in complex with VH domain antibody Deposited 2016-02-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 27–136（110 aa） Fragment：VEGF UNP RESIDUES 27-136
Chain W 27–136（110 aa） Fragment：VEGF UNP RESIDUES 27-136
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；0.1M TRIS PH 8.5, 7%PEG6000, 0.2M MGCL2 20C
Resolution 3.45 Å R-free 0.263
5FV2 Crystal structure of hVEGF in complex with VH domain antibody Deposited 2016-02-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain X 27–136（110 aa） Fragment：VEGF UNP RESIDUES 27-136
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；0.1M TRIS PH 8.5, 7%PEG6000, 0.2M MGCL2 20C
Resolution 3.45 Å R-free 0.263
5HHC Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21/n Deposited 2016-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 214–315（102 aa）
Chain B 214–315（102 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；Proteins were dissolved in 0.01 M HEPES at pH 7.0 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES (pH 7.0), 11% (v/v) PEG3350
Resolution 2.10 Å R-free 0.307
5HHD Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21 Deposited 2016-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 214–315（102 aa）
Chain B 214–315（102 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；Proteins were dissolved in 0.01 M HEPES at pH 7.0 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES (pH 7.0), 11% (v/v) PEG3350
Resolution 2.10 Å R-free 0.282
5O4E Crystal structure of VEGF in complex with heterodimeric Fcab JanusCT6 Deposited 2017-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 39–134（96 aa）
Chain F 39–134（96 aa）
Mutation：E13M Mutation：E13M MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 10 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 CAC CACODYLATE ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M Sodium cacodylate, 40% (v/v) MPD, 5% (w/v) PEG 8000
Resolution 2.15 Å R-free 0.236
5T89 Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6 Deposited 2016-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 27–147（121 aa）
Chain W 27–147（121 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；10-14% PEG3000 200 mM calcium chloride 100 mM MES pH 6.5
Resolution 4.00 Å R-free 0.315
6BFT Structure of Bevacizumab Fab mutant in complex with VEGF Deposited 2017-10-27 Different construct Different mutation/modification Different 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 34–135（102 aa） Fragment：residues 34-135
Chain B 34–135（102 aa） Fragment：residues 34-135
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v PEG 10000
Resolution 3.10 Å R-free 0.279
6T9D Crystal structure of a bispecific DutaFab in complex with human VEGF121 Deposited 2019-10-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain CCC 27–147（121 aa）
Chain DDD 27–147（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；VEGFA-121 from Peprotech, catalogue number 100-20A, was mixed at a 1:1 molar ratio to VEGF monomer. The complex was concentrated to 11 mg/ml. Crystallization involved hanging drop vapour diffusion against 0.1 M MES pH 6.5 and 1.6 M magnesium sulphate. Crystals grew in about 120 days and were frozen in liquid nitrogen with 20 % glycerol as cryoprotectant.
Resolution 2.90 Å R-free 0.280
6V7K Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-109) with one copy of HH4, an alpha/beta-Peptide with Irregular Secondary Structure Deposited 2019-12-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 34–135（102 aa）
Chain B 34–135（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v PEG 10000
Resolution 2.50 Å R-free 0.278
6Z13 VEGF-A 13:107 crystallized with 3C bicyclic peptide Deposited 2020-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain V 39–133（95 aa）
Chain W 39–133（95 aa）
Not recorded NH2 AMINO GROUP × 1 ACY ACETIC ACID × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；(VEGF)2:2 peptide_3C complex purified on SEC and concentrated at 9.8mg/ml in Tris/HCl 10mM pH 8.5. Mix of 1ul of complex with 1 ul of reservoir : NaOAc/HCl 100mM pH 4.6 / MPD 36% (v/v) / CaCl2 20mM
Resolution 1.80 Å R-free 0.247
6Z3F VEGF-A 13:107 crystallized with 2C bicyclic peptide Deposited 2020-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain V 39–133（95 aa）
Chain W 39–133（95 aa）
Not recorded NH2 AMINO GROUP × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 ACY ACETIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；(VEGF)2:2 PEPTIDE_3C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 / MPD 35% (V/V) / (NH4)2PO4 150MM
Resolution 2.10 Å R-free 0.265
6ZBR VEGF-A 13:107 crystallized with 4C bicyclic peptide Deposited 2020-06-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain V 39–133（95 aa）
Chain W 39–133（95 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；(VEGF)2:2 PEPTIDE_4C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 / MPD 35% (V/V) / (NH4)2PO4 150MM
Resolution 1.60 Å R-free 0.241
6ZCD VEGF-A 13:107 crystallized with 1C bicyclic peptide Deposited 2020-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain V 39–133（95 aa）
Chain W 39–133（95 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；(VEGF)2:2 PEPTIDE_1C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 13.5MG/ML IN TRIS/HCL 10MM PH 8.5. MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 / MPD 35% (V/V) / (NH4)2PO4 150MM
Resolution 1.80 Å R-free 0.242
6ZFL High resolution structure of VEGF-A 12:107 crystallized in tetragonal form Deposited 2020-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain V 219–313（95 aa）
Chain W 219–313（95 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；(VEGF)2:2 PEPTIDE_2C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. (SEE ID 6Z3F) mix 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : TRIS/HCL 100MM PH 8.5 / MPD 42% (V/V) / (NH4)2PO4 200MM
Resolution 1.60 Å R-free 0.186
7LL8 D-Protein RFX-V1 Bound to the VEGFR1 Domain 2 Site on VEGF-A Deposited 2021-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 214–315（102 aa）
Chain B 214–315（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.2 K；calcium chloride, Tris, PEG4000
Resolution 2.31 Å R-free 0.314
7LL9 D-Protein RFX-V2 Bound to the VEGFR1 Domain 3 Site on VEGF-A Deposited 2021-02-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 214–315（102 aa）
Chain B 214–315（102 aa）
Chain E 214–315（102 aa）
Chain F 214–315（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.2 K；magnesium chloride, Bis-Tris, PEG3350
Resolution 2.90 Å R-free 0.315
8UWZ The structure of Raamsizumab in complex with VEGF121 Deposited 2023-11-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 27–147（121 aa）
Chain F 27–147（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；298 K；0.2 M Sodium Phosphate mono basic, 30% PEG600
Resolution 3.50 Å R-free 0.298
9JU1 Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A Deposited 2024-10-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 214–315（102 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions COUNTER-DIFFUSION；pH 8；277 K；0.1M Tris-HCl pH 8.0, 0.2M NaCl, 2.5M Ammonium Sulfate, 0.04% NaN3
Resolution 1.45 Å R-free 0.245
9KKU Helix-loop-helix peptide (M49) in complex with VEGF-A Deposited 2024-11-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 214–315（102 aa）
Chain B 214–315（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions COUNTER-DIFFUSION；pH 5.6；293 K；0.2M NH4-AcOH pH 5.6, 14% PEG 3350, 20% 2-Propanol, 0.2M CaCl2,, 0.4M NaCl, 0.04% NaN3
Resolution 1.46 Å R-free 0.250

50 other PDB entries and 70 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 169–218； UniProt 183–232 Author chain B； PDBConstruct 169–218； UniProt 183–232

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 4deq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4deq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4deq
Deposition date deposition_date2012-01-21
Structure title titleStructure of the Neuropilin-1/VEGF-A complex
Keywords keywordsCoagulation factor domain, heparin binding domain, Angiogenesis, PROTEIN BINDING-CYTOKINE complex; PROTEIN BINDING/CYTOKINE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.34 Å
Radius of gyration Rg (electron density) rg_electron26.35 Å
Forward intensity I(0) i044037700.00
Molecular weight molecular_weight49021.0 kDa
Excluded volume excluded_volume60452 ų
Envelope volume envelope_volume82439 ų
Hydration-shell volume shell_volume26586 ų
Envelope diameter envelope_diameter91.7 Å
Shell Rg shell_rg32.72 Å
Envelope Rg envelope_rg26.44 Å
Shape Rg shape_rg26.27 Å
Total Rg total_rg27.30 Å
Total atoms total_atoms3429
Residues n_residues432
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 dmax87.4 Å
Rg (real space) rg_real27.28 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real4.4040e+07
I(0) uncertainty (real space) i0_real_error5.9060e+05
Rg (reciprocal space) rg_reciprocal27.30 Å
I(0) (reciprocal space) i0_reciprocal44040000.0000
Solution quality estimate total_estimate0.9106
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.7 Å
Skewness Skewness skewness0.181
Kurtosis Kurtosis kurtosis-0.576
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4222000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.984
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4deqA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id4deqA02
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
Domain ID domain_id4deqB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id4deqB02
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 (1)

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9. Files and Curves (10)