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5l7n

Plexin A1 extracellular fragment, domains 7-10 (IPT3-IPT6)

Method: X-RAY DIFFRACTION Dmax: 103.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Plexin-A1

Mus musculus

UniProt P70206

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 861–1241 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.5 K；25% (w/v) polyethylene glycol 3,350, 100mM BIS-TRIS pH 5.5 and 200mM potassium sodium tartrate Resolution 2.20 Å R-free 0.270

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 5L7N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RYT The Plexin A1 intracellular region in complex with Rac1 Deposited 2011-05-11 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 1269–1894（626 aa） Fragment：intracellular region (UNP residues 1269-1894)
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；15% PEG1500, 100 mM SPG buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.58 Å R-free 0.340
3RYT The Plexin A1 intracellular region in complex with Rac1 Deposited 2011-05-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1269–1894（626 aa） Fragment：intracellular region (UNP residues 1269-1894)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；15% PEG1500, 100 mM SPG buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.58 Å R-free 0.340
5L56 Plexin A1 full extracellular region, domains 1 to 10, to 4 angstrom Deposited 2016-05-28 Different construct 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 37–1236（1200 aa） Fragment：UNP residues 37-1236
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.5 K；6% (w/v) PEG 4k, 5 mM tricine or 5 mM TRIS
Resolution 4.00 Å R-free 0.308
5L59 Plexin A1 full extracellular region, domains 1 to 10, to 6 angstrom, spacegroup P2(1) Deposited 2016-05-28 Different construct 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 37–1236（1200 aa） Fragment：UNP residues 37-1236
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.5 K；15% (v/v) propanol, 20 mM magnesium chloride 50 mM MES, pH 6.0
Resolution 6.00 Å R-free 0.299
5L59 Plexin A1 full extracellular region, domains 1 to 10, to 6 angstrom, spacegroup P2(1) Deposited 2016-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 37–1236（1200 aa） Fragment：UNP residues 37-1236
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.5 K；15% (v/v) propanol, 20 mM magnesium chloride 50 mM MES, pH 6.0
Resolution 6.00 Å R-free 0.299
5L5C Plexin A1 full extracellular region, domains 1 to 10, to 6 angstrom, spacegroup P4(3)2(1)2 Deposited 2016-05-28 Different construct 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 37–1236（1200 aa） Fragment：UNP residues 37-1236
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；293.5 K；6% (w/v) PEG 4k, 5 mM tricine, pH 8.5
Resolution 6.00 Å R-free 0.316

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

View Construct and Data Evidence
UniProt name PLXA1_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–384； UniProt 861–1241

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 5l7n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5l7n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5l7n
Deposition date deposition_date2016-06-03
Structure title titlePlexin A1 extracellular fragment, domains 7-10 (IPT3-IPT6)
Keywords keywordsIPT domain, signaling protein, receptor, axon guidance; 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_guinier30.51 Å
Radius of gyration Rg (electron density) rg_electron30.74 Å
Forward intensity I(0) i024401200.00
Molecular weight molecular_weight38308.0 kDa
Excluded volume excluded_volume47888 ų
Envelope volume envelope_volume67291 ų
Hydration-shell volume shell_volume19481 ų
Envelope diameter envelope_diameter102.4 Å
Shell Rg shell_rg35.46 Å
Envelope Rg envelope_rg30.61 Å
Shape Rg shape_rg30.73 Å
Total Rg total_rg31.25 Å
Total atoms total_atoms2691
Residues n_residues344
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 dmax103.2 Å
Rg (real space) rg_real30.86 Å
Rg uncertainty (real space) rg_real_error1.02 Å
I(0) (real space) i0_real2.4400e+07
I(0) uncertainty (real space) i0_real_error3.8240e+05
Rg (reciprocal space) rg_reciprocal30.72 Å
I(0) (reciprocal space) i0_reciprocal24400000.0000
Solution quality estimate total_estimate0.7579
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.9 Å
Skewness Skewness skewness0.416
Kurtosis Kurtosis kurtosis-0.748
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3273000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.578; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.295; Smooth: 0.819
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)