SAXSdb — 5d3y

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 245–408	Fragment：unp residues 245-408	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 245–408	Fragment：unp residues 245-408	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

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 5D3Y	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 ligand/ion 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 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 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 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	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 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 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 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 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
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 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	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
6VSK Crystal structure of the P-Rex1 DEP1 domain Deposited 2020-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 409–499（91 aa） Fragment：P-Rex1DEP1 domain (UNP residues 409-499)	Not recorded	No recorded non-water small molecule	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
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 ligand/ion 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 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 18 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 4–167； UniProt 245–408 Author chain B； PDBConstruct 4–167； UniProt 245–408

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	5d3y
Deposition date deposition_date	2015-08-06
Structure title title	Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound
Keywords keywords	pleckstrin homology domain, beta sandwich, phosphatidylinositol-binding, LIPID BINDING PROTEIN; LIPID BINDING 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	25.14 Å
Radius of gyration Rg (electron density) rg_electron	24.57 Å
Forward intensity I(0) i0	20013300.00
Molecular weight molecular_weight	32562.0 kDa
Excluded volume excluded_volume	40222 Å³
Envelope volume envelope_volume	52226 Å³
Hydration-shell volume shell_volume	18952 Å³
Envelope diameter envelope_diameter	84.5 Å
Shell Rg shell_rg	30.01 Å
Envelope Rg envelope_rg	24.66 Å
Shape Rg shape_rg	24.56 Å
Total Rg total_rg	25.29 Å
Total atoms total_atoms	2278
Residues n_residues	272
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	83.5 Å
Rg (real space) rg_real	25.32 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	2.0010e+07
I(0) uncertainty (real space) i0_real_error	2.6920e+05
Rg (reciprocal space) rg_reciprocal	25.27 Å
I(0) (reciprocal space) i0_reciprocal	20010000.0000
Solution quality estimate total_estimate	0.8368
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.466
Kurtosis Kurtosis kurtosis	-0.519
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2816000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.670; Smooth: 0.969

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
Molecular weight formula_weight	19287.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2548

GEFEKLEALEQLQSHIEGWEGSNLTDICTQLLLQGTLLKISAGNIQERAFFLFDNLLVYCKRKSRVTGSKKSTKRTKSINGSLYIFRGRINTEVMEVENVEDGTADYHSNGYTVTNGWKIHNTAKNKWFVCMAKTAEEKQKWLDAIIREREQRESLKLGMERDAYVM

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 non-polymer

Description description	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
Molecular weight formula_weight	500.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5d3ya_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.0 — automated matches

Domain ID domain_id	d5d3yb_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5d3yA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	5d3yB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	59.686 Å
Unit-cell length b length_b	72.859 Å
Unit-cell length c length_c	77.939 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	29.780 Å
R factor r_factor	0.2100
R_work r_work	0.2074
R_free r_free	0.2584

fit	/app/data/saxs_computation/d3/5d3y/5d3y.fit
pddf	/app/data/pr_computation/d3/5d3y/5d3y.pr.out
profile	/app/data/saxs_computation/d3/5d3y/5d3y.dat

Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound

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