SAXSdb — 5c2j

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

Rac GTPase-activating protein 1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 346–546	Fragment：GAP domain, UNP residues 346-546	Cell division control protein 42 homolog × 1 （P60766） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG3350, Bis-Tris	Resolution 2.50 Å R-free 0.263

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 5C2J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OVJ The crystal structure of the human Rac GTPase activating protein 1 (RACGAP1) MgcRacGAP. Deposited 2007-02-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 348–546（199 aa） Fragment：Rho-GAP domain	Not recorded	7PE 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；25% PEG 3350, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.49 Å R-free 0.176
3W6R Crystal structure of the GAP domain of human MgcRacGAP Deposited 2013-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 348–546（199 aa） Fragment：Rho-GAP domain, UNP RESIDUES 348-546	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；295 K；100mM sodium cacodylate buffer, 13% polyethylene glycol 6000, 25% glycerol, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.90 Å R-free 0.259
3WPQ crystal structure of the GAP domain of MgcRacGAP(S387A) Deposited 2014-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 346–546（201 aa） Fragment：UNP residues 346-546	Mutation：S387A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.0M Na Citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.84 Å R-free 0.200
3WPQ crystal structure of the GAP domain of MgcRacGAP(S387A) Deposited 2014-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 346–546（201 aa） Fragment：UNP residues 346-546	Mutation：S387A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.0M Na Citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.84 Å R-free 0.200
3WPS crystal structure of the GAP domain of MgcRacGAP(S387D) Deposited 2014-01-15	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 346–546（201 aa） Fragment：UNP residues 346-546 Chain B 346–546（201 aa） Fragment：UNP residues 346-546	Mutation：S387D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：S387D Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；2.0M magnesium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.259
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	GOL GLYCEROL × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
5C2K Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP Deposited 2015-06-16	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 346–546（201 aa） Fragment：GAP domain, UNP residues 346-546	Mutation：S249D	MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG3350, Bis-Tris	Resolution 1.42 Å R-free 0.206

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RGAP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–208； UniProt 346–546

Cell division control protein 42 homolog

Mus musculus

UniProt P60766

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 1–191	Not recorded	Rac GTPase-activating protein 1 × 1 （Q9H0H5） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG3350, Bis-Tris	Resolution 2.50 Å R-free 0.263

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 5C2J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3EG5 Crystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP Deposited 2008-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–178（178 aa） Fragment：UNP residues 1-178 Chain C 1–178（178 aa） Fragment：UNP residues 1-178	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Bis-Tris-Propane (PH 8.8 adjusted with citric acid), 26% (w/v) PEG 3350, 250mM Na-Tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.243

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

View Construct and Data Evidence

UniProt name	CDC42_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 8–198； UniProt 1–191

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	5c2j
Deposition date deposition_date	2015-06-16
Structure title title	Complex structure of the GAP domain of MgcRacGAP and Cdc42
Keywords keywords	GTPase activation, Complex, small G-protein, HYDROLASE ACTIVATOR-SIGNALING PROTEIN complex; HYDROLASE ACTIVATOR/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	22.74 Å
Radius of gyration Rg (electron density) rg_electron	21.92 Å
Forward intensity I(0) i0	32355600.00
Molecular weight molecular_weight	44453.0 kDa
Excluded volume excluded_volume	56049 Å³
Envelope volume envelope_volume	65759 Å³
Hydration-shell volume shell_volume	24874 Å³
Envelope diameter envelope_diameter	82.4 Å
Shell Rg shell_rg	28.90 Å
Envelope Rg envelope_rg	22.19 Å
Shape Rg shape_rg	21.91 Å
Total Rg total_rg	22.85 Å
Total atoms total_atoms	3113
Residues n_residues	392
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	76.5 Å
Rg (real space) rg_real	22.70 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	3.2360e+07
I(0) uncertainty (real space) i0_real_error	4.5290e+05
Rg (reciprocal space) rg_reciprocal	22.71 Å
I(0) (reciprocal space) i0_reciprocal	32360000.0000
Solution quality estimate total_estimate	0.7925
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.337
Kurtosis Kurtosis kurtosis	-0.266
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7052000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	Rac GTPase-activating protein 1
Molecular weight formula_weight	23192.9 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	3216

GSSGSSGIGEGMLADFVSQTSPMIPSIVVHCVNEIEQRGLTETGLYRISGCDRTVKELKEKFLRVKTVPLLSKVDDIHAICSLLKDFLRNLKEPLLTFRLNRAFMEAAEITDEDNSIAAMYQAVGELPQANRDTLAFLMIHLQRVAQSPHTKMDVANLAKVFGPTIVAHAVPNPDPVTMSQDIKRQPKVVERLLSLPLEYWSQFMMVE

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

Entity 2 Entity 2 polymer

Description description	Cell division control protein 42 homolog
Molecular weight formula_weight	21803.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSSGSSGMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALEPPEPKKSRRCVLL

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 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	103

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5c2ja_
Class class	a — All alpha proteins
Fold Fold fold	a.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
Family Family family	a.116.1.0 — automated matches

Domain ID domain_id	d5c2jb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (2 domains)

Domain ID domain_id	5c2jA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

Domain ID domain_id	5c2jB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	43.324 Å
Unit-cell length b length_b	74.237 Å
Unit-cell length c length_c	55.423 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	32.390 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2630

fit	/app/data/saxs_computation/c2/5c2j/5c2j.fit
pddf	/app/data/pr_computation/c2/5c2j/5c2j.pr.out
profile	/app/data/saxs_computation/c2/5c2j/5c2j.dat

Complex structure of the GAP domain of MgcRacGAP and Cdc42

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

Rac GTPase-activating protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Cell division control protein 42 homolog

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)