SAXSdb — 2dls

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

Rho guanine nucleotide exchange factor 11

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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 44–123	Fragment：PDZ domain	No other associated polymer	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

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 2DLS	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 experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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
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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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
5E6P PlexinB2 cytoplasmic region/PDZ-RhoGEF PDZ domain complex Deposited 2015-10-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 42–125（84 aa） Fragment：PDZ domain (UNP residues 42-125)	Not recorded	No recorded non-water small molecule	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
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 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 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–87； UniProt 44–123

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	2dls
Deposition date deposition_date	2006-04-20
Structure title title	Solution structure of the PDZ domain of human Rho guanine nucleotide exchange factor 11
Keywords keywords	;PDZ domain, Rho guanine nucleotide exchange factor 11, PDZ-RhoGEF, ARHGEF11, KIAA0380, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.07 Å
Radius of gyration Rg (electron density) rg_electron	13.34 Å
Forward intensity I(0) i0	519832000.00
Molecular weight molecular_weight	188360.0 kDa
Excluded volume excluded_volume	235090 Å³
Envelope volume envelope_volume	33210 Å³
Hydration-shell volume shell_volume	16076 Å³
Envelope diameter envelope_diameter	61.2 Å
Shell Rg shell_rg	23.76 Å
Envelope Rg envelope_rg	18.47 Å
Shape Rg shape_rg	13.33 Å
Total Rg total_rg	13.67 Å
Total atoms total_atoms	26900
Residues n_residues	1860
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	53.5 Å
Rg (real space) rg_real	14.07 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	5.1980e+08
I(0) uncertainty (real space) i0_real_error	6.4030e+06
Rg (reciprocal space) rg_reciprocal	14.07 Å
I(0) (reciprocal space) i0_reciprocal	519800000.0000
Solution quality estimate total_estimate	0.7024
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	0.176
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	236900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.408; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.000

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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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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2dlsa1
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2dlsa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2dlsa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2dlsA00
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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Description description	Rho guanine nucleotide exchange factor 11
Molecular weight formula_weight	9441.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	26900

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	Cell free synthesis

fit	/app/data/saxs_computation/dl/2dls/2dls.fit
pddf	/app/data/pr_computation/dl/2dls/2dls.pr.out
profile	/app/data/saxs_computation/dl/2dls/2dls.dat

Solution structure of the PDZ domain of human Rho guanine nucleotide exchange factor 11

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

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)