SAXSdb — 3okt

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 35–703	Fragment：residues 33-703, extracellular domains 1-4	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 35–703	Fragment：residues 33-703, extracellular domains 1-4	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

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 3OKT	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 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 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 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 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 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
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 mutation/modification 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 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 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 4–672； UniProt 35–703

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	3okt
Deposition date deposition_date	2010-08-25
Structure title title	Mouse Plexin A2, extracellular domains 1-4
Keywords keywords	Transmembrane, receptor, sema-domain, Cell-cell signalling, Semaphorin-6A, 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	34.79 Å
Radius of gyration Rg (electron density) rg_electron	34.84 Å
Forward intensity I(0) i0	89773700.00
Molecular weight molecular_weight	74589.0 kDa
Excluded volume excluded_volume	93035 Å³
Envelope volume envelope_volume	123140 Å³
Hydration-shell volume shell_volume	32891 Å³
Envelope diameter envelope_diameter	129.5 Å
Shell Rg shell_rg	36.74 Å
Envelope Rg envelope_rg	35.85 Å
Shape Rg shape_rg	34.81 Å
Total Rg total_rg	35.10 Å
Total atoms total_atoms	5235
Residues n_residues	656
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	125.3 Å
Rg (real space) rg_real	35.35 Å
Rg uncertainty (real space) rg_real_error	1.63 Å
I(0) (real space) i0_real	8.9770e+07
I(0) uncertainty (real space) i0_real_error	1.7810e+06
Rg (reciprocal space) rg_reciprocal	35.00 Å
I(0) (reciprocal space) i0_reciprocal	89740000.0000
Solution quality estimate total_estimate	0.7405
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.4 Å
Skewness Skewness skewness	0.711
Kurtosis Kurtosis kurtosis	-0.195
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7456000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.441; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.519; Smooth: 0.781

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5417

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 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	182

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3oktA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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8. Citations (1)

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Unit-cell length a length_a	157.860 Å
Unit-cell length b length_b	92.903 Å
Unit-cell length c length_c	62.904 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.296 Å
Low-resolution limit resolution_low	44.907 Å
R factor r_factor	0.1986
R_work r_work	0.1958
R_free r_free	0.2506

fit	/app/data/saxs_computation/ok/3okt/3okt.fit
pddf	/app/data/pr_computation/ok/3okt/3okt.pr.out
profile	/app/data/saxs_computation/ok/3okt/3okt.dat

Mouse Plexin A2, extracellular domains 1-4

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

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

Diffraction experiment Diffraction