SAXSdb — 6vsk

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

Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 409–499	Fragment：P-Rex1DEP1 domain (UNP residues 409-499)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.1 M HEPES, pH 6.5, 45% w/v poly(acrylic acid sodium salt)2100	Resolution 3.12 Å R-free 0.233

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 6VSK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QIK Crystal structure of the first PDZ domain of PREX1 Deposited 2011-01-27	Different construct 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 607–706（100 aa） Fragment：UNP Residues 607-706	Not recorded	UNX UNKNOWN LIGAND × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；1.2M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate, pH 6.2, vapor diffusion, sitting drop, temperature 293K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；1.2M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate. Soaked for 6 hours in 0.01 M potassium hexaiodoplatin-(IV)-ate and mother liquor, pH 5.6, vapor diffusion, sitting drop, temperature 293K	Resolution 2.29 Å R-free 0.269
4YON P-Rex1:Rac1 complex Deposited 2015-03-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–404（404 aa） Fragment：UNP residues 1-404	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 sodium MES, pH 6.5, 0.2M sodium acetate, 15% (w/v) PEG 8000	Resolution 1.95 Å R-free 0.183
5D27 Crystal Structure of the P-Rex1 PH domain Deposited 2015-08-05	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 245–408（164 aa）	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；294 K；Bis Tris, Magnesium chloride, PEG 3350	Resolution 1.92 Å R-free 0.232
5D3V Crystal Structure of the P-Rex1 PH domain with Citrate Bound Deposited 2015-08-06	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 245–408（164 aa） Fragment：unp residues 245-408	Not recorded	FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；294 K；Sodium citrate, PEG 8000	Resolution 1.85 Å R-free 0.215
5D3V Crystal Structure of the P-Rex1 PH domain with Citrate Bound Deposited 2015-08-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 245–408（164 aa） Fragment：unp residues 245-408	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；294 K；Sodium citrate, PEG 8000	Resolution 1.85 Å R-free 0.215
5D3W Crystal Structure of the P-Rex1 PH domain with Sulfate Bound Deposited 2015-08-06	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 245–408（164 aa） Fragment：unp residues 245-408	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；294 K；Bis Tris, Ammonium sulfate, PEG 3350	Resolution 1.85 Å R-free 0.215
5D3W Crystal Structure of the P-Rex1 PH domain with Sulfate Bound Deposited 2015-08-06	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 245–408（164 aa） Fragment：unp residues 245-408	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；294 K；Bis Tris, Ammonium sulfate, PEG 3350	Resolution 1.85 Å R-free 0.215
5D3X Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound Deposited 2015-08-06	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 245–408（164 aa） Fragment：unp residues 245-408	Not recorded	4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；HEPES, Jeffamine ED-2001 pH 7	Resolution 1.69 Å R-free 0.214
5D3X Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound Deposited 2015-08-06	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 245–408（164 aa） Fragment：unp residues 245-408	Not recorded	4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；HEPES, Jeffamine ED-2001 pH 7	Resolution 1.69 Å R-free 0.214
5D3Y Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound Deposited 2015-08-06	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 245–408（164 aa） Fragment：unp residues 245-408	Not recorded	4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；294 K；Bis Tris, polypropylene glycol P400	Resolution 1.95 Å R-free 0.258
5D3Y Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound Deposited 2015-08-06	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 245–408（164 aa） Fragment：unp residues 245-408	Not recorded	4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；294 K；Bis Tris, polypropylene glycol P400	Resolution 1.95 Å R-free 0.258
5FI0 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1 Deposited 2015-12-22	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 38–201（164 aa） Chain A 202–408（207 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；Sodium dihydrogen phosphate, PEG 8000	Resolution 3.28 Å R-free 0.235
5FI0 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1 Deposited 2015-12-22	Different construct Different mutation/modification 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 38–201（164 aa） Chain C 202–408（207 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；Sodium dihydrogen phosphate, PEG 8000	Resolution 3.28 Å R-free 0.235
5FI0 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1 Deposited 2015-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 38–201（164 aa） Chain E 202–408（207 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；Sodium dihydrogen phosphate, PEG 8000	Resolution 3.28 Å R-free 0.235
5FI0 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1 Deposited 2015-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 38–201（164 aa） Chain G 202–408（207 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；Sodium dihydrogen phosphate, PEG 8000	Resolution 3.28 Å R-free 0.235
5FI1 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42 Deposited 2015-12-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 38–201（164 aa） Chain A 202–408（207 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；Ammonium citrate, PEG 3350	Resolution 3.20 Å R-free 0.198
7RX9 Structure of autoinhibited P-Rex1 Deposited 2021-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 41–305（265 aa） Chain A 323–502（180 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.8 M (NH4)2SO4, 0.05 MES pH 6.0	Resolution 3.22 Å R-free 0.262
7SYF Reconstruction of full-length Prex-1 (PtdIns(3,4,5)P3-dependent Rac Exchanger 1) Deposited 2021-11-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 41–305（265 aa） Chain A 323–1117（795 aa） Chain A 1212–1659（448 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8TUA Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4) Deposited 2023-08-15	Different construct 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 35–1659（1625 aa）	Not recorded	4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

12 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PREX1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–94； UniProt 409–499

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	6vsk
Deposition date deposition_date	2020-02-11
Structure title title	Crystal structure of the P-Rex1 DEP1 domain
Keywords keywords	DEP domain, P-Rex1, metastasis, domain-swapped, 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	23.22 Å
Radius of gyration Rg (electron density) rg_electron	23.19 Å
Forward intensity I(0) i0	2318770.00
Molecular weight molecular_weight	10677.0 kDa
Excluded volume excluded_volume	13427 Å³
Envelope volume envelope_volume	22849 Å³
Hydration-shell volume shell_volume	10017 Å³
Envelope diameter envelope_diameter	74.0 Å
Shell Rg shell_rg	25.61 Å
Envelope Rg envelope_rg	22.14 Å
Shape Rg shape_rg	23.12 Å
Total Rg total_rg	23.87 Å
Total atoms total_atoms	750
Residues n_residues	91
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	75.5 Å
Rg (real space) rg_real	23.46 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	2.3190e+06
I(0) uncertainty (real space) i0_real_error	3.2210e+04
Rg (reciprocal space) rg_reciprocal	23.41 Å
I(0) (reciprocal space) i0_reciprocal	2319000.0000
Solution quality estimate total_estimate	0.8467
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.360
Kurtosis Kurtosis kurtosis	-0.734
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	152300.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.591; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	103.152 Å
Unit-cell length b length_b	103.152 Å
Unit-cell length c length_c	67.981 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 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	3.120 Å
Low-resolution limit resolution_low	19.620 Å
R factor r_factor	0.1855
R_work r_work	0.1829
R_free r_free	0.2332

Description description	Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
Molecular weight formula_weight	10969.7 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	754

Crystal structure of the P-Rex1 DEP1 domain

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

Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein

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 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

fit	/app/data/saxs_computation/vs/6vsk/6vsk.fit
pddf	/app/data/pr_computation/vs/6vsk/6vsk.pr.out
profile	/app/data/saxs_computation/vs/6vsk/6vsk.dat