3i97

B1 domain of human Neuropilin-1 bound with small molecule EG00229

Method: X-RAY DIFFRACTION D_max: 71.3 Å Quality: EXCELLENT

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

Neuropilin-1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 273–427	Fragment：domain B1, F5/8 type C 1	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 273–427	Fragment：domain B1, F5/8 type C 1	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

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 3I97	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
2QQI Crystal Structure of the b1b2 Domains from Human Neuropilin-1 Deposited 2007-07-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 273–586（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
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 40 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 4–158； UniProt 273–427 Author chain B； PDBConstruct 4–158； UniProt 273–427

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3i97
Deposition date deposition_date	2009-07-10
Structure title title	B1 domain of human Neuropilin-1 bound with small molecule EG00229
Keywords keywords	;Neuropilin-1, Drug, VEGF, Angiogenesis, Neuropilin, Alternative splicing, Cell membrane, Developmental protein, Differentiation, Disulfide bond, Glycoprotein, Heparan sulfate, Membrane, Neurogenesis, Phosphoprotein, Polymorphism, Proteoglycan, Receptor, Secreted, Transmembrane, MEMBRANE PROTEIN, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.22 Å
Radius of gyration Rg (electron density) rg_electron	22.47 Å
Forward intensity I(0) i0	22372600.00
Molecular weight molecular_weight	35920.0 kDa
Excluded volume excluded_volume	44838 Å³
Envelope volume envelope_volume	53335 Å³
Hydration-shell volume shell_volume	20233 Å³
Envelope diameter envelope_diameter	72.5 Å
Shell Rg shell_rg	28.53 Å
Envelope Rg envelope_rg	22.51 Å
Shape Rg shape_rg	22.41 Å
Total Rg total_rg	23.42 Å
Total atoms total_atoms	2525
Residues n_residues	308
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	71.3 Å
Rg (real space) rg_real	23.21 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.2370e+07
I(0) uncertainty (real space) i0_real_error	2.9530e+05
Rg (reciprocal space) rg_reciprocal	23.22 Å
I(0) (reciprocal space) i0_reciprocal	22370000.0000
Solution quality estimate total_estimate	0.9104
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.668
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3498000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Neuropilin-1
Molecular weight formula_weight	17917.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2533

GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid
Molecular weight formula_weight	497.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3i97a_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.2 — Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain)

Domain ID domain_id	d3i97b_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.2 — Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain)

CATH v4.4 (2 domains)

Domain ID domain_id	3i97A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	3i97B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

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8. Citations (1)

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Unit-cell length a length_a	41.000 Å
Unit-cell length b length_b	89.600 Å
Unit-cell length c length_c	41.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	30.330 Å
R factor r_factor	0.2190
R_work r_work	0.2160
R_free r_free	0.2820

fit	/app/data/saxs_computation/i9/3i97/3i97.fit
pddf	/app/data/pr_computation/i9/3i97/3i97.pr.out
profile	/app/data/saxs_computation/i9/3i97/3i97.dat