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2qqi

Crystal Structure of the b1b2 Domains from Human Neuropilin-1

Method: X-RAY DIFFRACTION Dmax: 81.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neuropilin-1

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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 273–586 Fragment：F5/8 type C 1 and C 2 domains 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

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 2QQI 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 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
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
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 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 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
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 274–429（156 aa） Fragment：Neuropilin b1 domain/VEGF-A Heparin Binding Domain
Chain B 274–429（156 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 274–429（156 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 274–429（156 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
4RN5 B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site Deposited 2014-10-23 Different construct 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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）
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 41 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 5–318； UniProt 273–586

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 2qqi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qqi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2qqi
Deposition date deposition_date2007-07-26
Structure title titleCrystal Structure of the b1b2 Domains from Human Neuropilin-1
Keywords keywords;VEGF receptor, semaphorin receptor, Angiogenesis, Developmental protein, Differentiation, Glycoprotein, Heparan sulfate, Membrane, Neurogenesis, Proteoglycan, Secreted, Transmembrane, HORMONE, SIGNALING PROTEIN ;; SIGNALING PROTEIN
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_guinier23.55 Å
Radius of gyration Rg (electron density) rg_electron22.62 Å
Forward intensity I(0) i022695300.00
Molecular weight molecular_weight35848.0 kDa
Excluded volume excluded_volume44739 ų
Envelope volume envelope_volume54692 ų
Hydration-shell volume shell_volume21126 ų
Envelope diameter envelope_diameter83.6 Å
Shell Rg shell_rg28.47 Å
Envelope Rg envelope_rg22.88 Å
Shape Rg shape_rg22.63 Å
Total Rg total_rg23.34 Å
Total atoms total_atoms2520
Residues n_residues315
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 dmax81.4 Å
Rg (real space) rg_real23.65 Å
Rg uncertainty (real space) rg_real_error0.76 Å
I(0) (real space) i0_real2.2700e+07
I(0) uncertainty (real space) i0_real_error3.2850e+05
Rg (reciprocal space) rg_reciprocal23.63 Å
I(0) (reciprocal space) i0_reciprocal22690000.0000
Solution quality estimate total_estimate0.8511
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.2 Å
Skewness Skewness skewness0.451
Kurtosis Kurtosis kurtosis-0.362
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4976000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.852; Smooth: 0.951
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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) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2qqia1
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.2 — Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain)
Domain ID domain_idd2qqia2
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.2 — Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain)
Domain ID domain_idd2qqia3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id2qqiA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id2qqiA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
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8. Citations (1)

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9. Files and Curves (10)