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3al9

Mouse Plexin A2 extracellular domain

Method: X-RAY DIFFRACTION Dmax: 148.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Plexin-A2

Mus musculus

UniProt P70207

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 31–561 Chain B； UniProt 31–561 Fragment：sema and PSI domain (UNP RESIDUES 31-561) 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 31–561 Fragment：sema and PSI domain (UNP RESIDUES 31-561) 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 31–561 Fragment：sema and PSI domain (UNP RESIDUES 31-561) 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

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 3AL9 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 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 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
3OKT Mouse Plexin A2, extracellular domains 1-4 Deposited 2010-08-25 Different construct 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 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 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
4GZA Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1 Deposited 2012-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain A 33–703（671 aa） Fragment：UNP RESIDUES 33-703
Chain B 33–703（671 aa） Fragment：UNP RESIDUES 33-703
Chain C 33–703（671 aa） Fragment：UNP RESIDUES 33-703
Chain D 33–703（671 aa） Fragment：UNP RESIDUES 33-703
Chain E 33–703（671 aa） Fragment：UNP RESIDUES 33-703
Chain F 33–703（671 aa） Fragment：UNP RESIDUES 33-703
Not recorded 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
5L5G Plexin A2 full extracellular region, domains 1 to 8 modeled, data to 10 angstrom Deposited 2016-05-28 Different construct 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 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 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 9 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 1–531； UniProt 31–561 Author chain B； PDBConstruct 1–531； UniProt 31–561

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 3al9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3al9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3al9
Deposition date deposition_date2010-07-28
Structure title titleMouse Plexin A2 extracellular domain
Keywords keywordsbeta-propeller, Membrane protein, 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_guinier38.19 Å
Radius of gyration Rg (electron density) rg_electron37.86 Å
Forward intensity I(0) i0206013000.00
Molecular weight molecular_weight115790.0 kDa
Excluded volume excluded_volume144820 ų
Envelope volume envelope_volume184110 ų
Hydration-shell volume shell_volume43646 ų
Envelope diameter envelope_diameter157.0 Å
Shell Rg shell_rg40.28 Å
Envelope Rg envelope_rg38.32 Å
Shape Rg shape_rg37.78 Å
Total Rg total_rg38.29 Å
Total atoms total_atoms8144
Residues n_residues1032
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 dmax148.4 Å
Rg (real space) rg_real38.84 Å
Rg uncertainty (real space) rg_real_error2.11 Å
I(0) (real space) i0_real2.0600e+08
I(0) uncertainty (real space) i0_real_error4.0870e+06
Rg (reciprocal space) rg_reciprocal38.44 Å
I(0) (reciprocal space) i0_reciprocal205900000.0000
Solution quality estimate total_estimate0.7530
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.2 Å
Skewness Skewness skewness0.742
Kurtosis Kurtosis kurtosis0.234
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28980000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.423; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.553; Smooth: 0.963
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3al9A01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3al9A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily10 — ligand-binding face of the semaphorins, domain 2
Domain ID domain_id3al9B01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3al9B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily10 — ligand-binding face of the semaphorins, domain 2
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8. Citations (1)

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9. Files and Curves (10)