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5l5g

Plexin A2 full extracellular region, domains 1 to 8 modeled, data to 10 angstrom

Method: X-RAY DIFFRACTION Dmax: 235.9 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 33–1231 Chain C； UniProt 33–1231 Fragment：UNP residues 33-1231 No other associated polymer 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 33–1231 Chain D； UniProt 33–1231 Fragment：UNP residues 33-1231 No other associated polymer 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

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 5L5G 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 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 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
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
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 10 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 2–1200； UniProt 33–1231 Author chain B； PDBConstruct 2–1200； UniProt 33–1231 Author chain C； PDBConstruct 2–1200； UniProt 33–1231 Author chain D； PDBConstruct 2–1200； UniProt 33–1231

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 5l5g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5l5g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5l5g
Deposition date deposition_date2016-05-28
Structure title titlePlexin A2 full extracellular region, domains 1 to 8 modeled, data to 10 angstrom
Keywords keywordsreceptor, signaling, axon guidance, 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_guinier84.15 Å
Radius of gyration Rg (electron density) rg_electron84.99 Å
Forward intensity I(0) i02432020000.00
Molecular weight molecular_weight409950.0 kDa
Excluded volume excluded_volume510340 ų
Envelope volume envelope_volume1033500 ų
Hydration-shell volume shell_volume111880 ų
Envelope diameter envelope_diameter297.7 Å
Shell Rg shell_rg66.03 Å
Envelope Rg envelope_rg83.28 Å
Shape Rg shape_rg84.98 Å
Total Rg total_rg84.70 Å
Total atoms total_atoms28787
Residues n_residues3701
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 dmax235.9 Å
Rg (real space) rg_real80.74 Å
Rg uncertainty (real space) rg_real_error1.20 Å
I(0) (real space) i0_real2.3710e+09
I(0) uncertainty (real space) i0_real_error4.5590e+07
Rg (reciprocal space) rg_reciprocal81.92 Å
I(0) (reciprocal space) i0_reciprocal2416000000.0000
Solution quality estimate total_estimate0.8963
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary99.3 Å
Skewness Skewness skewness0.284
Kurtosis Kurtosis kurtosis-0.347
Angular range angular_range— – 0.0950 Å−1
Current regularization parameter α current_alpha0.1679
Highest regularization parameter α highest_alpha59490000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 0.979; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.306
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)