SAXSdb — 5e6p

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

Plexin-B2

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1226–1842	Fragment：UNP residues 1226-1842	Rho guanine nucleotide exchange factor 11 × 1 （O15085）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；0.2 M K/Na tartrate, 0.1 M Na citrate pH 5.3, 1.4 M ammonium sulfate	Resolution 3.21 Å R-free 0.297

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 5E6P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7KDC The complex between RhoD and the Plexin B2 RBD Deposited 2020-10-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1463–1565（103 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M MgCl2, 22 % (w/v) PEG 3350, and 100 mM MIB (pH 6.8, sodium malonate, imidazole, and boric acid mixed at 2:3:3 molar ratio).	Resolution 3.10 Å R-free 0.266
7KDC The complex between RhoD and the Plexin B2 RBD Deposited 2020-10-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1463–1565（103 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M MgCl2, 22 % (w/v) PEG 3350, and 100 mM MIB (pH 6.8, sodium malonate, imidazole, and boric acid mixed at 2:3:3 molar ratio).	Resolution 3.10 Å R-free 0.266

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLXB2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–621； UniProt 1226–1842

Rho guanine nucleotide exchange factor 11

Homo sapiens

UniProt O15085

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 42–125	Fragment：PDZ domain (UNP residues 42-125)	Plexin-B2 × 1 （B2RXS4）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；0.2 M K/Na tartrate, 0.1 M Na citrate pH 5.3, 1.4 M ammonium sulfate	Resolution 3.21 Å R-free 0.297

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 5E6P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HTJ STRUCTURE OF THE RGS-LIKE DOMAIN FROM PDZ-RHOGEF Deposited 2000-12-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 281–490（210 aa） Fragment：RGS-LIKE DOMAIN (RESIDUES 281-490)	Mutation：K463A, E465A, E466A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Ammonium Sulfate, PEG 400, Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.258
1XCG Crystal Structure of Human RhoA in complex with DH/PH fragment of PDZRHOGEF Deposited 2004-09-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 714–1081（368 aa） Fragment：DH/PH domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；PEG, Hepes, pH 7.2, VAPOR DIFFUSION, temperature 298K	Resolution 2.50 Å R-free 0.281
1XCG Crystal Structure of Human RhoA in complex with DH/PH fragment of PDZRHOGEF Deposited 2004-09-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 714–1081（368 aa） Fragment：DH/PH domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；PEG, Hepes, pH 7.2, VAPOR DIFFUSION, temperature 298K	Resolution 2.50 Å R-free 0.281
2DLS Solution structure of the PDZ domain of human Rho guanine nucleotide exchange factor 11 Deposited 2006-04-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 44–123（80 aa） Fragment：PDZ domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.20mM U-15N, 13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3KZ1 Crystal Structure of the Complex of PDZ-RhoGEF DH/PH domains with GTP-gamma-S Activated RhoA Deposited 2009-12-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 710–1085（376 aa） Fragment：UNP residues 710-1085	Not recorded	MG MAGNESIUM ION × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；14-16% PEG 10000, 0.1M ammonium acetate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.283
3KZ1 Crystal Structure of the Complex of PDZ-RhoGEF DH/PH domains with GTP-gamma-S Activated RhoA Deposited 2009-12-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 710–1085（376 aa） Fragment：UNP residues 710-1085	Not recorded	MG MAGNESIUM ION × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；14-16% PEG 10000, 0.1M ammonium acetate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.283
3T06 Crystal Structure of the DH/PH fragment of PDZRHOGEF with N-terminal regulatory elements in complex with Human RhoA Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 672–1081（410 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.15 M DL-malic acid, 20 % w/v PEG 3350, pH 7.0, vapor diffusion, sitting drop, temperature 298K	Resolution 2.84 Å R-free 0.257
3T06 Crystal Structure of the DH/PH fragment of PDZRHOGEF with N-terminal regulatory elements in complex with Human RhoA Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 672–1081（410 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.15 M DL-malic acid, 20 % w/v PEG 3350, pH 7.0, vapor diffusion, sitting drop, temperature 298K	Resolution 2.84 Å R-free 0.257
5JHG Crystal structure of the complex between the human RhoA and the DH/PH domain of human ARHGEF11 Deposited 2016-04-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 714–1081（368 aa） Fragment：UNP residues 714-1081	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；2% v/v Tacsimate pH 5.0, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 16% PEG 3350	Resolution 2.50 Å R-free 0.270
5JHG Crystal structure of the complex between the human RhoA and the DH/PH domain of human ARHGEF11 Deposited 2016-04-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 714–1081（368 aa） Fragment：UNP residues 714-1081	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；2% v/v Tacsimate pH 5.0, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 16% PEG 3350	Resolution 2.50 Å R-free 0.270
5JHH Crystal structure of the ternary complex between the human RhoA, its inhibitor and the DH/PH domain of human ARHGEF11 Deposited 2016-04-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 714–1081（368 aa） Fragment：UNP residues 714-1081	Not recorded	GOL GLYCEROL × 2 RA0 3-{3-[ethyl(quinolin-2-yl)amino]phenyl}propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；2% v/v Tacsimate pH 5.0, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 16% PEG 3350	Resolution 2.30 Å R-free 0.239
5JHH Crystal structure of the ternary complex between the human RhoA, its inhibitor and the DH/PH domain of human ARHGEF11 Deposited 2016-04-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 714–1081（368 aa） Fragment：UNP residues 714-1081	Not recorded	GOL GLYCEROL × 1 RA0 3-{3-[ethyl(quinolin-2-yl)amino]phenyl}propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；2% v/v Tacsimate pH 5.0, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 16% PEG 3350	Resolution 2.30 Å R-free 0.239
5TYT Crystal Structure of the PDZ domain of RhoGEF bound to CXCR2 C-terminal peptide Deposited 2016-11-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 41–123（83 aa） Fragment：Rho (UNP residues 41-123), CXCR2 C-terminal peptide (UNP residues 356-360) Chain B 41–123（83 aa） Fragment：Rho (UNP residues 41-123), CXCR2 C-terminal peptide (UNP residues 356-360)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG8000, 0.1 M sodium citrate, 0.2 M sodium acetate	Resolution 2.40 Å R-free 0.240
5TYT Crystal Structure of the PDZ domain of RhoGEF bound to CXCR2 C-terminal peptide Deposited 2016-11-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 41–123（83 aa） Fragment：Rho (UNP residues 41-123), CXCR2 C-terminal peptide (UNP residues 356-360) Chain D 41–123（83 aa） Fragment：Rho (UNP residues 41-123), CXCR2 C-terminal peptide (UNP residues 356-360)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG8000, 0.1 M sodium citrate, 0.2 M sodium acetate	Resolution 2.40 Å R-free 0.240

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARHGB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–88； UniProt 42–125

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	5e6p
Deposition date deposition_date	2015-10-10
Structure title title	PlexinB2 cytoplasmic region/PDZ-RhoGEF PDZ domain complex
Keywords keywords	Plexin, PDZ, PDZ-RhoGEF, Complex, 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	30.31 Å
Radius of gyration Rg (electron density) rg_electron	29.61 Å
Forward intensity I(0) i0	60719700.00
Molecular weight molecular_weight	63484.0 kDa
Excluded volume excluded_volume	80424 Å³
Envelope volume envelope_volume	104730 Å³
Hydration-shell volume shell_volume	30557 Å³
Envelope diameter envelope_diameter	99.9 Å
Shell Rg shell_rg	35.53 Å
Envelope Rg envelope_rg	29.64 Å
Shape Rg shape_rg	29.58 Å
Total Rg total_rg	30.29 Å
Total atoms total_atoms	4478
Residues n_residues	579
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	98.5 Å
Rg (real space) rg_real	30.37 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	6.0720e+07
I(0) uncertainty (real space) i0_real_error	9.2800e+05
Rg (reciprocal space) rg_reciprocal	30.34 Å
I(0) (reciprocal space) i0_reciprocal	60720000.0000
Solution quality estimate total_estimate	0.8906
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.3 Å
Skewness Skewness skewness	0.317
Kurtosis Kurtosis kurtosis	-0.632
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	13390000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.921; Smooth: 0.946

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Plexin-B2
Molecular weight formula_weight	71868.7 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	4478

GPHMRKSQQAEREYEKIKSQLEGLEESVRDRCKKEFTDLMIEMEDQTNDVHEAGIPTLDYKTYTDRVFFLPSKDGDKDVMITGKLDIPESRRPIVEQALYQFSNLLNSKSFLINFIHTLENQREFSARAKVYFASLLTVALHGKLEYYTDIMRTLFLELMEQYVVAKNPKLMLRRSETVVERMLSNWMSICLYQYLKDSAGEPLYKLFKAIKHQVEKGPVDAVQKKAKYTLNDTGLLGDDVEYAPLTVSVIVQDEGIDAIPVKVLNCDTISQVKEKIIDQVYRTQPCSCWPKPDSVVLEWRPGSTAQILSDLDLTSQREGRWKRINTLMHYNVRDGATLILSKVGVSQQPEDSQQDLPGERHALLEEENRVWHLVRPTDEVDEGKSKRGSMKEKERTKAITEIYLTRLLSVKGTLQQFVDNFFQSVLAPGHAVPPAVKYFFDFLDEQAEKHDIRDEDTIHIWKTNSLPLRFWVNILKNPHFIFDVHVHEVVDASLSVIAQTFMDACTRTEHKLSRDSPSNKLLYAKEISTYKKMVEDYYKGIRQMVQVSDQDMNTHLAEISRAHTDSLNTLVALHQLYQYTQKYYDEIINALEEDPAAQKMQLAFRLQQIAAALENKVTDL

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Rho guanine nucleotide exchange factor 11
Molecular weight formula_weight	9227.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPHMGLVQRCVIIQKDQHGFGFTVSGDRIVLVQSVRPGGAAMKAGVKEGDRIIKVNGTMVTNSSHLEVVKLIKSGAYVALTLLGSSPS

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	Escherichia coli

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5e6pA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	506 — GTPase Activation - p120GAP; domain 1
Homologous superfamily homologous superfamily	10 — GTPase Activation - p120gap; domain 1

Domain ID domain_id	5e6pA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	5e6pB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (1)

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Unit-cell length a length_a	126.152 Å
Unit-cell length b length_b	126.152 Å
Unit-cell length c length_c	211.465 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	3.215 Å
Low-resolution limit resolution_low	48.530 Å
R factor r_factor	0.2562
R_work r_work	0.2542
R_free r_free	0.2966

fit	/app/data/saxs_computation/e6/5e6p/5e6p.fit
pddf	/app/data/pr_computation/e6/5e6p/5e6p.pr.out
profile	/app/data/saxs_computation/e6/5e6p/5e6p.dat

PlexinB2 cytoplasmic region/PDZ-RhoGEF PDZ domain complex

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

Plexin-B2

State in the Current Structure

Other States of the Same Protein in the Database

Rho guanine nucleotide exchange factor 11

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)