SAXSdb — 5ih2

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

Adapter molecule crk

Mus musculus

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 134–191	Fragment：UNP residues 134-191	Proline rich Peptide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K	Resolution 1.80 Å R-free 0.243
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 134–191	Fragment：UNP residues 134-191	Proline rich Peptide × 1 NA SODIUM ION × 1 P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K	Resolution 1.80 Å R-free 0.243

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 5IH2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B07 CRK SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR Deposited 1998-11-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–190（57 aa） Fragment：SH3 DOMAIN	Not recorded	PYJ PHENYLETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；29% PEG4000, 0.2 M AMMONIUM ACETATE, PH 6.0, pH 6.00	Resolution 2.50 Å R-free 0.354
1CKA STRUCTURAL BASIS FOR THE SPECIFIC INTERACTION OF LYSINE-CONTAINING PROLINE-RICH PEPTIDES WITH THE N-TERMINAL SH3 DOMAIN OF C-CRK Deposited 1995-01-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–190（57 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å
1CKB STRUCTURAL BASIS FOR THE SPECIFIC INTERACTION OF LYSINE-CONTAINING PROLINE-RICH PEPTIDES WITH THE N-TERMINAL SH3 DOMAIN OF C-CRK Deposited 1995-01-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–190（57 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1JU5 Ternary complex of an Crk SH2 domain, Crk-derived phophopeptide, and Abl SH3 domain by NMR spectroscopy Deposited 2001-08-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 217–228（12 aa） Fragment：Crk phosphopeptide	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure ambient NMR sample composition 0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide \| 90% H2O/10% D2O	Resolution not provided
1M30 Solution structure of N-terminal SH3 domain from oncogene protein c-Crk Deposited 2002-06-26	Different construct Different mutation/modification 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 134–191（58 aa） Fragment：N-TERMINAL SH3 DOMAIN (residues 134-191)	Mutation：R191G	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；307 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient NMR sample composition 1mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O NMR sample composition 1mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O	Resolution not provided
1M3A Solution structure of a circular form of the truncated N-terminal SH3 domain from oncogene protein c-Crk. Deposited 2002-06-27	Different construct Different mutation/modification 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 135–191（57 aa） Fragment：N-TERMINAL SH3 DOMAIN (residues 135-191)	Mutation：R191G, E135C, deleted A134	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；307 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient NMR sample composition 1mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O NMR sample composition 1mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O	Resolution not provided
1M3B Solution structure of a circular form of the N-terminal SH3 domain (A134C, E135G, R191G mutant) from oncogene protein c-Crk. Deposited 2002-06-27	Different construct Different mutation/modification 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 134–191（58 aa） Fragment：N-TERMINAL SH3 DOMAIN (residues 134-191)	Mutation：R191G, E135G, A134C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；307 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient NMR sample composition 1mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O NMR sample composition 1mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O	Resolution not provided
1M3C Solution structure of a circular form of the N-terminal SH3 domain (E132C, E133G, R191G mutant) from oncogene protein c-Crk Deposited 2002-06-27	Different construct Different mutation/modification 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 132–191（60 aa） Fragment：N-TERMINAL SH3 DOMAIN (residues 132-191)	Mutation：R191G, added G133, C132	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；307 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient NMR sample composition 1mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O NMR sample composition 1mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3 \| 90% H2O/10% D2O	Resolution not provided
2GGR Solution structure of the C-terminal SH3 domain of c-CrkII Deposited 2006-03-24	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 230–304（75 aa） Fragment：C-terminal Domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 50mM；Pressure ambient NMR sample composition 0.4 mM cSH3 domain U-15N,13C; 10mM phosphate buffer pH7.2; 50mM NaCl; 5mM DTT-d10; 0.1% NaN3; 1mM EDTA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5JN0 CRK-II SH2 domain Deposited 2016-04-29	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 6–121（116 aa） Fragment：UNP residues 6-121	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；100 mM MES pH 6.5, 12% PEG 20,000	Resolution 1.68 Å R-free 0.210
5L23 Crystal structure of the complex between the N-terminal SH3 domain of CrkII and a proline-rich ligand Deposited 2016-07-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–191（58 aa） Fragment：UNP residues 134-191	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286 K；Lithium sulfate monohydrate, PEG 3350	Resolution 1.77 Å R-free 0.210

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CRK_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–58； UniProt 134–191 Author chain B； PDBConstruct 1–58； UniProt 134–191

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	5ih2
Deposition date deposition_date	2016-02-28
Structure title title	Structure, thermodynamics, and the role of conformational dynamics in the interactions between the N-terminal SH3 domain of CrkII and proline-rich motifs in cAbl
Keywords keywords	SH3 domain Polyproline II motif, 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	17.82 Å
Radius of gyration Rg (electron density) rg_electron	17.01 Å
Forward intensity I(0) i0	5111200.00
Molecular weight molecular_weight	16604.0 kDa
Excluded volume excluded_volume	20885 Å³
Envelope volume envelope_volume	24959 Å³
Hydration-shell volume shell_volume	12998 Å³
Envelope diameter envelope_diameter	68.5 Å
Shell Rg shell_rg	22.16 Å
Envelope Rg envelope_rg	17.49 Å
Shape Rg shape_rg	17.01 Å
Total Rg total_rg	17.96 Å
Total atoms total_atoms	1172
Residues n_residues	134
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	70.8 Å
Rg (real space) rg_real	17.91 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	5.1110e+06
I(0) uncertainty (real space) i0_real_error	6.9910e+04
Rg (reciprocal space) rg_reciprocal	17.90 Å
I(0) (reciprocal space) i0_reciprocal	5111000.0000
Solution quality estimate total_estimate	0.7640
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.2 Å
Skewness Skewness skewness	0.513
Kurtosis Kurtosis kurtosis	-0.037
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2081000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.435; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.623; Smooth: 1.000

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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	Adapter molecule crk
Molecular weight formula_weight	6971.7 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	1388

AEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYR

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 2 Entity 2 polymer

Description description	Proline rich Peptide
Molecular weight formula_weight	1285.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N

XYEKPALPRKRX

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
Molecular weight formula_weight	162.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ih2A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	5ih2B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Unit-cell length a length_a	45.222 Å
Unit-cell length b length_b	29.479 Å
Unit-cell length c length_c	45.756 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.31 °
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	1.800 Å
Low-resolution limit resolution_low	45.630 Å
R factor r_factor	0.1732
R_work r_work	0.1696
R_free r_free	0.2425

fit	/app/data/saxs_computation/ih/5ih2/5ih2.fit
pddf	/app/data/pr_computation/ih/5ih2/5ih2.pr.out
profile	/app/data/saxs_computation/ih/5ih2/5ih2.dat

Structure, thermodynamics, and the role of conformational dynamics in the interactions between the N-terminal SH3 domain of CrkII and proline-rich motifs in cAbl

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

Adapter molecule crk

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

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) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)