SAXSdb — 3ol2

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

Semaphorin-4D

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 12 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 22–677	Fragment：Extracellular domains	Plexin-B1 × 2 （O43157） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；294 K；0.1 M Tris,0.2 M calcium acetate, 6% v/v glycerol, 20% PEG3000, pH 7, VAPOR DIFFUSION, temperature 294K	Resolution 2.99 Å R-free 0.237

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 3OL2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OLZ The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D Deposited 2003-08-19	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 22–677（656 aa） Fragment：SOLUBLE EXTRACELLULAR FRAGMENT, RESIDUES 22-677 Chain B 22–677（656 aa） Fragment：SOLUBLE EXTRACELLULAR FRAGMENT, RESIDUES 22-677	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.2 M AMMONIUM FLORIDE, 20% PEG 3350, pH 7.50	Resolution 2.00 Å R-free 0.270

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SEM4D_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–656； UniProt 22–677

Plexin-B1

Homo sapiens

UniProt O43157

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 12 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 20–535	Fragment：Extracellular domainsl (1-2)	Semaphorin-4D × 2 （Q92854） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；294 K；0.1 M Tris,0.2 M calcium acetate, 6% v/v glycerol, 20% PEG3000, pH 7, VAPOR DIFFUSION, temperature 294K	Resolution 2.99 Å R-free 0.237

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 3OL2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JPH NMR solution structure of the Rho GTPase binding domain of human plexin-b1 Deposited 2007-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1743–1862（120 aa） Fragment：Sequence database residues 1743-1862	Mutation：W1830F	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1.75 mM [U-100% 13C; U-100% 15N] protein, 90%H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.25 mM [U-100% 13C; U-100% 15N; 80% 2H] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2OS6 Solution structure of LARG PDZ domain in complex with C-terminal octa-peptide of Plexin B1 Deposited 2007-02-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2128–2135（8 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 50 mM phosphate buffer, 50mM NaCl；Pressure 1 NMR sample composition 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 90% H2O, 10% D2O \| 50mM phosphate buffer, 90% H2O, 10% D2O NMR sample composition 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 99.9% D2O \| 50mM phosphate buffer, 99.9% D2O	Resolution not provided
2R2O Crystal structure of the effector domain of human Plexin B1 Deposited 2007-08-27	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 1743–1862（120 aa） Fragment：Effector domain: Residues 1743-1862 Chain B 1743–1862（120 aa） Fragment：Effector domain: Residues 1743-1862	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；291 K；2.6M Sodium chloride, 18% Ethylene glycol, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 291K	Resolution 2.00 Å R-free 0.269
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	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 1743–1862（120 aa） Fragment：Residues 1743-1862	Not recorded	UNX UNKNOWN LIGAND × 15 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1743–1862（120 aa） Fragment：Residues 1743-1862	Not recorded	UNX UNKNOWN LIGAND × 15 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1743–1862（120 aa） Fragment：Residues 1743-1862 Chain C 1743–1862（120 aa） Fragment：Residues 1743-1862	Not recorded	UNX UNKNOWN LIGAND × 30 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1743–1862（120 aa） Fragment：Residues 1743-1862 Chain C 1743–1862（120 aa） Fragment：Residues 1743-1862	Not recorded	UNX UNKNOWN LIGAND × 60 MG MAGNESIUM ION × 4 CA CALCIUM ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1743–1862（120 aa） Fragment：Residues 1743-1862 Chain C 1743–1862（120 aa） Fragment：Residues 1743-1862	Not recorded	UNX UNKNOWN LIGAND × 30 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
3HM6 Crystal structure of the cytoplasmic domain of human plexin B1 Deposited 2009-05-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 1511–2135（625 aa） Fragment：Cytoplasmic domain (UNP residues 1511-2135)	Mutation：S1625T	UNX UNKNOWN LIGAND × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；16% peg-2000 mme, 0.1M TRIS, 0.2M TMAO, pH 8, vapor diffusion, hanging drop, temperature 291K	Resolution 2.40 Å R-free 0.262
3SU8 Crystal structure of a truncated intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11	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 X 1533–2135（603 aa） Fragment：UNP residues 1533-2135	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.238
3SUA Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11	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 D 1511–2135（625 aa） Fragment：UNP residues 1533-2135	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.39 Å R-free 0.264
3SUA Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1511–2135（625 aa） Fragment：UNP residues 1533-2135	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.39 Å R-free 0.264
3SUA Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1511–2135（625 aa） Fragment：UNP residues 1533-2135	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.39 Å R-free 0.264
3SUA Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1511–2135（625 aa） Fragment：UNP residues 1533-2135 Chain E 1511–2135（625 aa） Fragment：UNP residues 1533-2135 Chain F 1511–2135（625 aa） Fragment：UNP residues 1533-2135	Not recorded	MG MAGNESIUM ION × 3 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.39 Å R-free 0.264
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19	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 20–535（516 aa） Fragment：UNP residues 20-535	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000	Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–535（516 aa） Fragment：UNP residues 20-535	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000	Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 20–535（516 aa） Fragment：UNP residues 20-535	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000	Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–535（516 aa） Fragment：UNP residues 20-535	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000	Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 20–535（516 aa） Fragment：UNP residues 20-535	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000	Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 20–535（516 aa） Fragment：UNP residues 20-535	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000	Resolution 2.60 Å R-free 0.265
7VF3 Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide Deposited 2021-09-10	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 19–535（517 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1M sodium acetate buffer, 20% PEG 400, 0.2M Calcium acetate	Resolution 2.29 Å R-free 0.226
7VF3 Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide Deposited 2021-09-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 19–535（517 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1M sodium acetate buffer, 20% PEG 400, 0.2M Calcium acetate	Resolution 2.29 Å R-free 0.226
7VG7 Plexin B1 extracellular fragment in complex with lasso-grafted PB1m6A9 peptide Deposited 2021-09-14	Different construct Different mutation/modification 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 19–535（517 aa）	Mutation：T19S	PGE TRIETHYLENE GLYCOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES or HEPES, 14-16% PEG 3350	Resolution 2.50 Å R-free 0.243
8B3K Crystal structure of human Plexin-B1 (20-535) in the unbound state Deposited 2022-09-16	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 20–535（516 aa） Chain B 20–535（516 aa）	Not recorded	CD CADMIUM ION × 14 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；1.0 M sodium acetate, 0.2 M cadmium sulphate, 0.1 M HEPES, pH 7.5	Resolution 2.69 Å R-free 0.245

11 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLXB1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–519； UniProt 20–535

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	3ol2
Deposition date deposition_date	2010-08-25
Structure title title	Receptor-ligand structure of Human Semaphorin 4D with Plexin B1.
Keywords keywords	Beta-Propeller, Signalling, Extacellular, 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	38.73 Å
Radius of gyration Rg (electron density) rg_electron	39.20 Å
Forward intensity I(0) i0	244564000.00
Molecular weight molecular_weight	125430.0 kDa
Excluded volume excluded_volume	156430 Å³
Envelope volume envelope_volume	208420 Å³
Hydration-shell volume shell_volume	47486 Å³
Envelope diameter envelope_diameter	155.9 Å
Shell Rg shell_rg	41.18 Å
Envelope Rg envelope_rg	40.08 Å
Shape Rg shape_rg	39.17 Å
Total Rg total_rg	39.42 Å
Total atoms total_atoms	8828
Residues n_residues	1110
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	145.8 Å
Rg (real space) rg_real	39.36 Å
Rg uncertainty (real space) rg_real_error	1.59 Å
I(0) (real space) i0_real	2.4460e+08
I(0) uncertainty (real space) i0_real_error	4.7480e+06
Rg (reciprocal space) rg_reciprocal	38.97 Å
I(0) (reciprocal space) i0_reciprocal	244500000.0000
Solution quality estimate total_estimate	0.7745
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.1 Å
Skewness Skewness skewness	0.737
Kurtosis Kurtosis kurtosis	0.225
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	34000000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.506; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.711; Smooth: 0.836

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Semaphorin-4D
Molecular weight formula_weight	74315.5 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	8828

MAFAPIPRITWEHREVHLVQFHEPDIYNYSALLLSEDKDTLYIGAREAVFAVNALNISEKQHEVYWKVSEDKKAKCAEKGKSKQTECLNYIRVLQPLSATSLYVCGTNAFQPACDHLNLTSFKFLGKNEDGKGRCPFDPAHSYTSVMVDGELYSGTSYNFLGSEPIISRNSSHSPLRTEYAIPWLNEPSFVFADVIRKSPDSPDGEDDRVYFFFTEVSVEYEFVFRVLIPRIARVCKGDQGGLRTLQKKWTSFLKARLICSRPDSGLVFNVLRDVFVLRSPGLKVPVFYALFTPQLNNVGLSAVCAYNLSTAEEVFSHGKYMQSTTVEQSHTKWVRYNGPVPKPRPGACIDSEARAANYTSSLNLPDKTLQFVKDHPLMDDSVTPIDNRPRLIKKDVNYTQIVVDRTQALDGTVYDVMFVSTDRGALHKAISLEHAVHIIEETQLFQDFEPVQTLLLSSKKGNRFVYAGSNSGVVQAPLAFCGKHGTCEDCVLARDPYCAWSPPTATCVALHQTESPSRGLIQEMSGDASVCPDKSKGSYRQHFFKHGGTAELKCSQKSNLARVFWKFQNGVLKAESPKYGLMGRKNLLIFNLSEGDSGVYQCLSEERVKNKTVFQVVAKHVLEVKVVPKPVVAPTLSVVQTEGSRIATKVLVASTKHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Plexin-B1
Molecular weight formula_weight	56924.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ETGLQPLPPTAFTPNGTYLQHLARDPTSGTLYLGATNFLFQLSPGLQLEATVSTGPVLDSRDCLPPVMPDECPQAQPTNNPNQLLLVSPGALVVCGSVHQGVCEQRRLGQLEQLLLRPERPGDTQYVAANDPAVSTVGLVAQGLAGEPLLFVGRGYTSRGVGGGIPPITTRALWPPDPQAAFSYEETAKLAVGRLSEYSHHFVSAFARGASAYFLFLRRDLQAQSRAFRAYVSRVCLRDQHYYSYVELPLACEGGRYGLIQAAAVATSREVAHGEVLFAAFSSAAPPTVGRPPSAAAGASGASALCAFPLDEVDRLANRTRDACYTREGRAEDGTEVAYIEYDVNSDCAQLPVDTLDAYPCGSDHTPSPMASRVPLEATPILEWPGIQLTAVAVTMEDGHTIAFLGDSQGQLHRVYLGPGSDGHPYSTQSIQQGSAVSRDLTFDGTFEHLYVMTQSTLLKVPVASCAQHLDCASCLAHRDPYCGWCVLLGRCSRRSECSRGQGPEQWLWSFQPELGCLQGTKHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	3

Entity 5 Entity 5 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	1

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3ol2a1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.12 — Sema domain
Family Family family	b.69.12.1 — Sema domain

Domain ID domain_id	d3ol2a2
Class class	g — Small proteins
Fold Fold fold	g.16 — Trefoil/Plexin domain-like
Superfamily Superfamily superfamily	g.16.2 — Plexin repeat
Family Family family	g.16.2.1 — Plexin repeat

Domain ID domain_id	d3ol2a3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

CATH v4.4 (5 domains)

Domain ID domain_id	3ol2A01
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

Domain ID domain_id	3ol2A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily	10 — ligand-binding face of the semaphorins, domain 2

Domain ID domain_id	3ol2A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3ol2B01
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

Domain ID domain_id	3ol2B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily	10 — ligand-binding face of the semaphorins, domain 2

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8. Citations (1)

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Unit-cell length a length_a	83.055 Å
Unit-cell length b length_b	173.436 Å
Unit-cell length c length_c	482.119 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	F 2 2 2
Space-group number int_tables_number	22
Crystal system crystal_system	—

Resolution resolution	2.990 Å
Low-resolution limit resolution_low	49.490 Å
R factor r_factor	0.1920
R_work r_work	0.1895
R_free r_free	0.2372

fit	/app/data/saxs_computation/ol/3ol2/3ol2.fit
pddf	/app/data/pr_computation/ol/3ol2/3ol2.pr.out
profile	/app/data/saxs_computation/ol/3ol2/3ol2.dat

Receptor-ligand structure of Human Semaphorin 4D with Plexin B1.

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

Semaphorin-4D

State in the Current Structure

Other States of the Same Protein in the Database

Plexin-B1

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)