SAXSdb — 2kg5

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

Arf-GAP, Rho-GAP domain, ANK repeat and PH domain-containing protein 3

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 1–80	Fragment：SAM Domain, residues 1-80	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.7；298 K；Pressure ambient NMR sample composition：1 mM protein, 2.7 mM potassium chloride, 137 mM sodium chloride, 11.9 mM phosphates, 0.3% mM sodium azide, 100% D2O \| 100% D2O NMR sample composition：1 mM [U-100% 15N] protein, 2.7 mM potassium chloride, 137 mM sodium chloride, 11.9 mM phosphates, 0.3% mM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：1 mM [U-100% 13C; U-100% 15N] protein, 2.7 mM potassium chloride, 137 mM sodium chloride, 11.9 mM phosphates, 0.3% mM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% 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 2KG5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LNW Identification and structural basis for a novel interaction between Vav2 and Arap3 Deposited 2012-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1404–1412（9 aa） Fragment：UNP RESIDUES 1404-1412	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 3 mM entity_2-2, 5 mM potassium phosphate-3, 20 mM sodium phosphate-4, 5 mM DTT-5, 2 mM EDTA-6, 75 mM sodium chloride-7, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-8, 3 mM entity_2-9, 5 mM potassium phosphate-10, 75 mM sodium chloride-11, 5 mM DTT-12, 2 mM EDTA-13, 20 mM sodium phosphate-14, 100% D2O \| 100% D2O	Resolution not provided
5JCP RhoGAP domain of ARAP3 in complex with RhoA in the transition state Deposited 2016-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 906–1107（202 aa） Fragment：UNP residues 906-1107,UNP residues 2-181	Mutation：F25N	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 15%(v/v) PEG 550 MME, 4%(v/v) Acetone	Resolution 2.10 Å R-free 0.227
5JCP RhoGAP domain of ARAP3 in complex with RhoA in the transition state Deposited 2016-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 906–1107（202 aa） Fragment：UNP residues 906-1107,UNP residues 2-181	Mutation：F25N	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 15%(v/v) PEG 550 MME, 4%(v/v) Acetone	Resolution 2.10 Å R-free 0.227
5JD0 crystal structure of ARAP3 RhoGAP domain Deposited 2016-04-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 906–1107（202 aa） Fragment：UNP residues 906-1107	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；100 mM HEPES, 10% PEG8000	Resolution 2.30 Å R-free 0.260
5JD0 crystal structure of ARAP3 RhoGAP domain Deposited 2016-04-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 906–1107（202 aa） Fragment：UNP residues 906-1107	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；100 mM HEPES, 10% PEG8000	Resolution 2.30 Å R-free 0.260
7A9B Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide Deposited 2020-09-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1414–1429（16 aa） Chain B 1414–1429（16 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 nL of protein solution (15 mg/ml mutant protein in 10 mM HEPES buffer, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol and 0.5 mM TCEP) were mixed with 100 nL reservoir buffer (16% (w/v) polyethylene glycol 3350 and 0.2 M ammonium citrate), above a reservoir volume of 20 microL	Resolution 2.00 Å R-free 0.249
7YIR Crystal structure of N-terminal PH domain of ARAP3 protein from human Deposited 2022-07-18	Different construct 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 284–385（102 aa） Fragment：PH1 domain	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS (pH 6.5), 30% v/v Polyethylene glycol monomethyl ether 550	Resolution 2.10 Å R-free 0.230
7YIS Crystal structure of N-terminal PH domain of ARAP3 protein in complex with inositol 1,3,4,5-tetrakisphosphate Deposited 2022-07-18	Different construct 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 284–385（102 aa） Fragment：PH1 domain	Not recorded	4PT (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate (pH 4.6), 30% v/v Polyethylene glycol 400	Resolution 3.30 Å R-free 0.276

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

View Construct and Data Evidence

UniProt name	ARAP3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–100； UniProt 1–80

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	2kg5
Deposition date deposition_date	2009-03-05
Structure title title	NMR Solution structure of ARAP3-SAM
Keywords keywords	;SAM DOMAIN, HELIX BUNDLE, Cell membrane, Cell projection, Cytoplasm, Cytoskeleton, GTPase activation, Membrane, Metal-binding, Phosphoprotein, Polymorphism, Zinc, Zinc-finger, 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	15.71 Å
Radius of gyration Rg (electron density) rg_electron	15.14 Å
Forward intensity I(0) i0	479858000.00
Molecular weight molecular_weight	175960.0 kDa
Excluded volume excluded_volume	217180 Å³
Envelope volume envelope_volume	41132 Å³
Hydration-shell volume shell_volume	17635 Å³
Envelope diameter envelope_diameter	76.5 Å
Shell Rg shell_rg	26.59 Å
Envelope Rg envelope_rg	23.03 Å
Shape Rg shape_rg	15.06 Å
Total Rg total_rg	15.71 Å
Total atoms total_atoms	24640
Residues n_residues	1620
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	43.6 Å
Rg (real space) rg_real	14.47 Å
Rg uncertainty (real space) rg_real_error	0.09 Å
I(0) (real space) i0_real	4.5600e+08
I(0) uncertainty (real space) i0_real_error	4.0590e+06
Rg (reciprocal space) rg_reciprocal	16.01 Å
I(0) (reciprocal space) i0_reciprocal	479900000.0000
Solution quality estimate total_estimate	0.6592
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.1 Å
Skewness Skewness skewness	0.438
Kurtosis Kurtosis kurtosis	-0.066
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	3.5310
Highest regularization parameter α highest_alpha	215900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.012; Oscil: 0.878; Stabil: 0.980; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; 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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2kg5A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

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8. Citations (1)

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Description description	Arf-GAP, Rho-GAP domain, ANK repeat and PH domain-containing protein 3
Molecular weight formula_weight	10864.2 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	24640

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

fit	/app/data/saxs_computation/kg/2kg5/2kg5.fit
pddf	/app/data/pr_computation/kg/2kg5/2kg5.pr.out
profile	/app/data/saxs_computation/kg/2kg5/2kg5.dat

NMR Solution structure of ARAP3-SAM

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

Arf-GAP, Rho-GAP domain, ANK repeat and PH domain-containing protein 3

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) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)