SAXSdb — 4gza

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

Plexin-A2

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain A； UniProt 33–703 Chain B； UniProt 33–703 Chain C； UniProt 33–703 Chain D； UniProt 33–703 Chain E； UniProt 33–703 Chain F； UniProt 33–703	Fragment：UNP RESIDUES 33-703	Semaphorin-3A × 2 （O08665） Neuropilin-1 × 2 （P97333） CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 1% v/v ethyl acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 8% v/v acetonitrile , VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 7.00 Å R-free 0.285

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 4GZA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3AL8 Plexin A2 / Semaphorin 6A complex Deposited 2010-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 31–561（531 aa） Fragment：sema and PSI domain (UNP RESIDUES 31-561)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；18-25% (wt./vol.) PEG 1000, 0.2-0.3M MgCl2, 0.1M Na-cacodylate pH 5.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.287
3AL8 Plexin A2 / Semaphorin 6A complex Deposited 2010-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 31–561（531 aa） Fragment：sema and PSI domain (UNP RESIDUES 31-561)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；18-25% (wt./vol.) PEG 1000, 0.2-0.3M MgCl2, 0.1M Na-cacodylate pH 5.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.287
3AL9 Mouse Plexin A2 extracellular domain Deposited 2010-07-28	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 31–561（531 aa） Fragment：sema and PSI domain (UNP RESIDUES 31-561) Chain B 31–561（531 aa） Fragment：sema and PSI domain (UNP RESIDUES 31-561)	Not recorded	EDO 1,2-ETHANEDIOL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；24-28%(wt/vol) PEG 3350, 0-0.2M NaCl, 0.1M Tris-Cl pH 8.0-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.257
3AL9 Mouse Plexin A2 extracellular domain Deposited 2010-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–561（531 aa） Fragment：sema and PSI domain (UNP RESIDUES 31-561)	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；24-28%(wt/vol) PEG 3350, 0-0.2M NaCl, 0.1M Tris-Cl pH 8.0-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.257
3AL9 Mouse Plexin A2 extracellular domain Deposited 2010-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–561（531 aa） Fragment：sema and PSI domain (UNP RESIDUES 31-561)	Not recorded	EDO 1,2-ETHANEDIOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；24-28%(wt/vol) PEG 3350, 0-0.2M NaCl, 0.1M Tris-Cl pH 8.0-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.257
3OKT Mouse Plexin A2, extracellular domains 1-4 Deposited 2010-08-25	Different construct Different mutation/modification 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 35–703（669 aa） Fragment：residues 33-703, extracellular domains 1-4	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CL CHLORIDE ION × 2 NA SODIUM ION × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Polyethylene Glycol 6000 12.8% w/v, Magnesium Chloride 128mM, HEPES 64mM pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.251
3OKT Mouse Plexin A2, extracellular domains 1-4 Deposited 2010-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 35–703（669 aa） Fragment：residues 33-703, extracellular domains 1-4	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CL CHLORIDE ION × 4 NA SODIUM ION × 2 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Polyethylene Glycol 6000 12.8% w/v, Magnesium Chloride 128mM, HEPES 64mM pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.251
3OKY Plexin A2 in complex with Semaphorin 6A Deposited 2010-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 33–701（669 aa） Fragment：residues 33-703, extracellular domains 1-4	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；2-Methyl-2,4-Pentanediol 12.4% v/v, MES 124mM pH 6.0, ethyl acetate 1% v/v, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.19 Å R-free 0.230
5L5G Plexin A2 full extracellular region, domains 1 to 8 modeled, data to 10 angstrom Deposited 2016-05-28	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 33–1231（1199 aa） Fragment：UNP residues 33-1231 Chain C 33–1231（1199 aa） Fragment：UNP residues 33-1231	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.5 K；0.68 M potassium/sodium tartrate, 85 mM HEPES, pH 7.5	Resolution 10.00 Å R-free 0.370
5L5G Plexin A2 full extracellular region, domains 1 to 8 modeled, data to 10 angstrom Deposited 2016-05-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 33–1231（1199 aa） Fragment：UNP residues 33-1231 Chain D 33–1231（1199 aa） Fragment：UNP residues 33-1231	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.5 K；0.68 M potassium/sodium tartrate, 85 mM HEPES, pH 7.5	Resolution 10.00 Å R-free 0.370
5L74 Plexin A2 extracellular segment domains 4-5 (PSI2-IPT2), resolution 1.36 Angstrom 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 monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 655–803（149 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.5 K；25% (w/v) polyethylene glycol 3,350 and 100 mM BIS-TRIS pH 5.5	Resolution 1.36 Å R-free 0.203

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLXA2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–672； UniProt 33–703 Author chain B； PDBConstruct 2–672； UniProt 33–703 Author chain C； PDBConstruct 2–672； UniProt 33–703 Author chain D； PDBConstruct 2–672； UniProt 33–703 Author chain E； PDBConstruct 2–672； UniProt 33–703 Author chain F； PDBConstruct 2–672； UniProt 33–703

Semaphorin-3A

Mus musculus

UniProt O08665

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain G； UniProt 21–555	Fragment：UNP RESIDUES 21-555	Plexin-A2 × 12 （P70207） Neuropilin-1 × 2 （P97333） CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 1% v/v ethyl acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 8% v/v acetonitrile , VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 7.00 Å R-free 0.285

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 4GZA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Q47 Structure of the Semaphorin 3A Receptor-Binding Module Deposited 2003-08-01	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 26–520（495 aa） Fragment：Sema-3A 65k (residues 26-520) Chain B 26–520（495 aa） Fragment：Sema-3A 65k (residues 26-520)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Tris, PEG 8000, heptyl-beta-D thioglucoside, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.294
4GZ8 Mouse Semaphorin 3A, domains Sema-PSI-IG Deposited 2012-09-06	Different construct Different mutation/modification 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 21–569（549 aa） Fragment：UNP RESIDUES 21-675 Chain B 21–569（549 aa） Fragment：UNP RESIDUES 21-675	Not recorded	CA CALCIUM ION × 5 ACT ACETATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M sodium cacodylate, 0.1M calcium acetate, 12% w/v PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.265
7M0R Cryo-EM structure of the Sema3A/PlexinA4/Neuropilin 1 complex Deposited 2021-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 21–569（549 aa） Chain D 21–569（549 aa）	Mutation：A106K,551ARTRA555,731AAQAA735,758ANRA761 Mutation：A106K,551ARTRA555,731AAQAA735,758ANRA761	CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SEM3A_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 4–538； UniProt 21–555

Neuropilin-1

Mus musculus

UniProt P97333

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain H； UniProt 22–586	Fragment：UNP RESIDUES 22-586	Plexin-A2 × 12 （P70207） Semaphorin-3A × 2 （O08665） CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 1% v/v ethyl acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 8% v/v acetonitrile , VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 7.00 Å R-free 0.285

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 4GZA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10RI Dimeric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 22–855（834 aa） Chain F 22–855（834 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.60 Å
10RJ Heparin-induced cis tetrameric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain E 22–855（834 aa） Chain F 22–855（834 aa） Chain K 22–855（834 aa） Chain L 22–855（834 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.34 Å
10RK Heparin-induced trans tetrameric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain E 22–855（834 aa） Chain F 22–855（834 aa） Chain K 22–855（834 aa） Chain L 22–855（834 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.65 Å
4GZ9 Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2) Deposited 2012-09-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–586（565 aa） Fragment：UNP RESIDUES 22-586	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES, pH 7.5, 1.5M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.223
4GZ9 Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2) Deposited 2012-09-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–586（565 aa） Fragment：UNP RESIDUES 22-586	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 4 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES, pH 7.5, 1.5M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.223
7M0R Cryo-EM structure of the Sema3A/PlexinA4/Neuropilin 1 complex Deposited 2021-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 22–588（567 aa） Chain F 22–588（567 aa）	Not recorded	CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NRP1_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 4–568； UniProt 22–586

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4gza
Deposition date deposition_date	2012-09-06
Structure title title	Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1
Keywords keywords	ternary complex, multi-domain, mammalian, cell-cell signaling, glycosilation, transmembrane, 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	69.34 Å
Radius of gyration Rg (electron density) rg_electron	69.58 Å
Forward intensity I(0) i0	3626400000.00
Molecular weight molecular_weight	507010.0 kDa
Excluded volume excluded_volume	632730 Å³
Envelope volume envelope_volume	998670 Å³
Hydration-shell volume shell_volume	120220 Å³
Envelope diameter envelope_diameter	240.1 Å
Shell Rg shell_rg	69.47 Å
Envelope Rg envelope_rg	67.76 Å
Shape Rg shape_rg	69.59 Å
Total Rg total_rg	69.54 Å
Total atoms total_atoms	35655
Residues n_residues	4537
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	241.0 Å
Rg (real space) rg_real	69.44 Å
Rg uncertainty (real space) rg_real_error	2.70 Å
I(0) (real space) i0_real	3.6260e+09
I(0) uncertainty (real space) i0_real_error	7.8530e+07
Rg (reciprocal space) rg_reciprocal	68.84 Å
I(0) (reciprocal space) i0_reciprocal	3622000000.0000
Solution quality estimate total_estimate	0.8572
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.9 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-0.569
Angular range angular_range	— – 0.1150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	251900000.0000
Real-space data points n_real_points	24
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.614

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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	Plexin-A2
Molecular weight formula_weight	75934.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	35655

ETGMPQYSTFHSENRDWTFNHLTVHRRTGAVYVGAINRVYKLTGNLTIQVAHKTGPEEDNKACYPPLIVQPCSEVLTLTNNVNKLLIIDYSENRLLACGSLYQGVCKLLRLDDLFILVEPSHKKEHYLSSVNKTGTMYGVIVRSEGEDGKLFIGTAVDGKQDYFPTLSSRKLPRDPESSAMLDYELHSDFVSSLIKIPSDTLALVSHFDIFYIYGFASGGFVYFLTVQPETPDGMAINSAGDLFYTSRIVRLCKDDPKFHSYVSLPFGCTRAGVEYRLLQAAYLAKPGEALAQAFNISSDEDVLFAIFSKGQKQYHHPPDDSALCAFPIRAINLQIKERLQSCYHGEGNLELNWLLGKDVQCTKAPVPIDDNFCGLDINQPLGGSTPVEGLTLYTTSRDRLTSVASYVYNGYSVVFVGTKSGKLKKIRADGPPHGGVQYEMVSVFKDGSPILRDMAFSINQLYLYVMSERQVTRVPVESCEQYTTCGECLSSGDPHCGWCALHNMCSRRDKCQRAWEANRFAASISQCMSLEVHPNSISVSDHSRLLSLVVNDAPNLSEGIACAFGNLTEVEGQVSGSQVICISPGPKDVPVIPLDQDWFGLELQLRSKETGKIFVSTEFKFYNCSAHQLCLSCVNSAFRCHWCKYRNLCTHDPTTCSFQEGRINVSEDCPQGTKHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Semaphorin-3A
Molecular weight formula_weight	61246.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

ETGNYANGKNNVPRLKLSYKEMLESNNVITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIKDFQKIVWPVSYTRRDECKWAGKDILKECANFIKVLEAYNQTHLYACGTGAFHPICTYIEVGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDGELYSGTAADFMGRDFAIFRTLGHHHPIRTEQHDSRWLNDPRFISAHLIPESDNPEDDKVYFFFRENAIDGEHSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRRVFLGPYAHRDGPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRPIMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSVPKETWHDLEEVLLEEMTVFREPTTISAMELSTKQQQLYIGSTAGVAQLPLHRCDIYGKACAECCLARDPYCAWDGSSCSRYFPTAKRRTRR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Neuropilin-1
Molecular weight formula_weight	65467.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

ETGFRSDKCGGTIKIENPGYLTSPGYPHSYHPSEKCEWLIQAPEPYQRIMINFNPHFDLEDRDCKYDYVEVIDGENEGGRLWGKFCGKIAPSPVVSSGPFLFIKFVSDYETHGAGFSIRYEIFKRGPECSQNYTAPTGVIKSPGFPEKYPNSLECTYIIFAPKMSEIILEFESFDLEQDSNPPGGMFCRYDRLEIWDGFPEVGPHIGRYCGQKTPGRIRSSSGVLSMVFYTDSAIAKEGFSANYSVLQSSISEDFKCMEALGMESGEIHSDQITASSQYGTNWSVERSRLNYPENGWTPGEDSYKEWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYRVDISSNGEDWISLKEGNKAIIFQGNTNPTDVVLGVFSKPLITRFVRIKPVSWETGISMRFEVYGCKITDYPCSGMLGMVSGLISDSQITASNQADRNWMPENIRLVTSRTGWALPPSPHPYTNEWLQVDLGDEKIVRGVIIQGGKHRENKVFMRKFKIAYSNNGSDWKTIMDDSKRKAKSFEGNNNYDTPELRTFSPLSTRFIRIYPERATHSGLGLRMELLGCEVERTKHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	191.632 Å
Unit-cell length b length_b	293.604 Å
Unit-cell length c length_c	252.176 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	7.000 Å
Low-resolution limit resolution_low	125.506 Å
R factor r_factor	0.2847
R_work r_work	0.2847
R_free r_free	0.2848

fit	/app/data/saxs_computation/gz/4gza/4gza.fit
pddf	/app/data/pr_computation/gz/4gza/4gza.pr.out
profile	/app/data/saxs_computation/gz/4gza/4gza.dat

Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1

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

Plexin-A2

State in the Current Structure

Other States of the Same Protein in the Database

Semaphorin-3A

State in the Current Structure

Other States of the Same Protein in the Database

Neuropilin-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)