SAXSdb — 1wdz

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

insulin receptor substrate p53

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–228 Chain B； UniProt 1–228	Fragment：N-terminal domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；27% PEG4000, 0.09M Tris pH8.5, 0.19M Sodium acetate, 3.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.63 Å R-free 0.297

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 1WDZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y2O Structure of N-terminal domain IRSp53/BAIAP2 Deposited 2004-11-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–250（250 aa） Fragment：N-terminal domain Chain B 1–250（250 aa） Fragment：N-terminal domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.267
2YKT Crystal structure of the I-BAR domain of IRSp53 (BAIAP2) in complex with an EHEC derived Tir peptide Deposited 2011-05-30	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 1–250（250 aa） Fragment：I-BAR DOMAIN, RESIDUES 1-250	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 16% (W/V) PEG 3350, 0.3M AMMONIUM SULPHATE	Resolution 2.11 Å R-free 0.276
3RNJ Crystal structure of the SH3 domain from IRSp53 (BAIAP2) Deposited 2011-04-22	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 375–436（62 aa） Fragment：SH3 domain, UNP residues 375-436	Not recorded	EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2M ammonium acetate, 0.1M Tris-HCl pH 8.5, 30% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.50 Å R-free 0.219
4JS0 Complex of Cdc42 with the CRIB-PR domain of IRSp53 Deposited 2013-03-22	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 B 260–291（32 aa） Fragment：CRIB-PR domain	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 2 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；18-20% PEG 4000, 0.2M magnesium chloride, 0.004M betain hydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.199
6BD2 Complex of 14-3-3 theta with an IRSp53 peptide doubly-phosphorylated at T340 and S366 Deposited 2017-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 335–372（38 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PEG DI(HYDROXYETHYL)ETHER × 1 1PE PENTAETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M CaCl2, 13% Peg 3350	Resolution 2.90 Å R-free 0.254
6BQT Complex of 14-3-3 theta with an IRSp53 peptide doubly-phosphorylated at T340 and T360 Deposited 2017-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 335–366（32 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 1PE PENTAETHYLENE GLYCOL × 3 EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M CaCl2, 13% Peg 3350	Resolution 2.80 Å R-free 0.287
6BQT Complex of 14-3-3 theta with an IRSp53 peptide doubly-phosphorylated at T340 and T360 Deposited 2017-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 335–366（32 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 2 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M CaCl2, 13% Peg 3350	Resolution 2.80 Å R-free 0.287
6BQT Complex of 14-3-3 theta with an IRSp53 peptide doubly-phosphorylated at T340 and T360 Deposited 2017-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 335–366（32 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	1PE PENTAETHYLENE GLYCOL × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M CaCl2, 13% Peg 3350	Resolution 2.80 Å R-free 0.287
6BQT Complex of 14-3-3 theta with an IRSp53 peptide doubly-phosphorylated at T340 and T360 Deposited 2017-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 335–366（32 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	1PE PENTAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M CaCl2, 13% Peg 3350	Resolution 2.80 Å R-free 0.287
6ZEG Structure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to Phactr1 (516-580) Deposited 2020-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 448–464（17 aa）	Mutation：N-terminal Vector derived sequence GHMGS	MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% (w/v) polyethylene glycol 3350, 0.2 M KSCN and 0.1 M BIS-Tris propane pH 8.5	Resolution 1.09 Å R-free 0.140
6ZEG Structure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to Phactr1 (516-580) Deposited 2020-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 448–464（17 aa）	Mutation：N-terminal Vector derived sequence GHMGS	MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 2 16P 3,6,9,12,15,18-HEXAOXAICOSANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% (w/v) polyethylene glycol 3350, 0.2 M KSCN and 0.1 M BIS-Tris propane pH 8.5	Resolution 1.09 Å R-free 0.140
6ZEI Structure of PP1-IRSp53 S455E chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to Phactr1 (516-580) Deposited 2020-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 448–464（17 aa）	Mutation：N-terminal Vector derived sequence GHMGS	MN MANGANESE (II) ION × 2 GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；20% (w/v) polyethylene glycol 3350 and 0.2 M NaBr	Resolution 1.39 Å R-free 0.158
6ZEI Structure of PP1-IRSp53 S455E chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to Phactr1 (516-580) Deposited 2020-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 448–464（17 aa）	Mutation：N-terminal Vector derived sequence GHMGS	MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；20% (w/v) polyethylene glycol 3350 and 0.2 M NaBr	Resolution 1.39 Å R-free 0.158

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BAIP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–231； UniProt 1–228 Author chain B； PDBConstruct 4–231； UniProt 1–228

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	1wdz
Deposition date deposition_date	2004-05-21
Structure title title	Crystal structure of RCB domain of IRSp53
Keywords keywords	cellular signaling protein, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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	39.41 Å
Radius of gyration Rg (electron density) rg_electron	41.56 Å
Forward intensity I(0) i0	44302800.00
Molecular weight molecular_weight	51884.0 kDa
Excluded volume excluded_volume	64716 Å³
Envelope volume envelope_volume	88000 Å³
Hydration-shell volume shell_volume	23668 Å³
Envelope diameter envelope_diameter	185.5 Å
Shell Rg shell_rg	33.58 Å
Envelope Rg envelope_rg	44.29 Å
Shape Rg shape_rg	41.49 Å
Total Rg total_rg	41.18 Å
Total atoms total_atoms	3642
Residues n_residues	453
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	182.8 Å
Rg (real space) rg_real	41.27 Å
Rg uncertainty (real space) rg_real_error	4.28 Å
I(0) (real space) i0_real	4.4300e+07
I(0) uncertainty (real space) i0_real_error	9.0540e+05
Rg (reciprocal space) rg_reciprocal	40.09 Å
I(0) (reciprocal space) i0_reciprocal	44250000.0000
Solution quality estimate total_estimate	0.5407
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.933
Kurtosis Kurtosis kurtosis	0.443
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2938000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.008; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1wdza1
Class class	a — All alpha proteins
Fold Fold fold	a.238 — BAR/IMD domain-like
Superfamily Superfamily superfamily	a.238.1 — BAR/IMD domain-like
Family Family family	a.238.1.3 — IMD domain

Domain ID domain_id	d1wdza2
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	d1wdzb2
Class class	a — All alpha proteins
Fold Fold fold	a.238 — BAR/IMD domain-like
Superfamily Superfamily superfamily	a.238.1 — BAR/IMD domain-like
Family Family family	a.238.1.3 — IMD domain

Domain ID domain_id	d1wdzb3
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 (2 domains)

Domain ID domain_id	1wdzA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

Domain ID domain_id	1wdzB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

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8. Citations (1)

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Unit-cell length a length_a	60.833 Å
Unit-cell length b length_b	69.258 Å
Unit-cell length c length_c	68.715 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.12 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.630 Å
Low-resolution limit resolution_low	41.940 Å
R factor r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.2970

Description description	insulin receptor substrate p53
Molecular weight formula_weight	27597.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3712

Crystal structure of RCB domain of IRSp53

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

insulin receptor substrate p53

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

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

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	70

fit	/app/data/saxs_computation/wd/1wdz/1wdz.fit
pddf	/app/data/pr_computation/wd/1wdz/1wdz.pr.out
profile	/app/data/saxs_computation/wd/1wdz/1wdz.dat