SAXSdb — 5jn0

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

CRK-II SH2 domain

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 6–121	Fragment：UNP residues 6-121	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

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 5JN0	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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
5IH2 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 Deposited 2016-02-28	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 134–191（58 aa） Fragment：UNP residues 134-191	Not recorded	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
5IH2 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 Deposited 2016-02-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 134–191（58 aa） Fragment：UNP residues 134-191	Not recorded	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
5L23 Crystal structure of the complex between the N-terminal SH3 domain of CrkII and a proline-rich ligand Deposited 2016-07-30	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 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 12 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 1–99； UniProt 6–121

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	5jn0
Deposition date deposition_date	2016-04-29
Structure title title	CRK-II SH2 domain
Keywords keywords	SH2 domain, PROTEIN BINDING; PROTEIN BINDING
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	14.77 Å
Radius of gyration Rg (electron density) rg_electron	13.01 Å
Forward intensity I(0) i0	2755640.00
Molecular weight molecular_weight	11125.0 kDa
Excluded volume excluded_volume	13772 Å³
Envelope volume envelope_volume	16000 Å³
Hydration-shell volume shell_volume	10600 Å³
Envelope diameter envelope_diameter	47.5 Å
Shell Rg shell_rg	18.69 Å
Envelope Rg envelope_rg	13.52 Å
Shape Rg shape_rg	12.97 Å
Total Rg total_rg	14.39 Å
Total atoms total_atoms	785
Residues n_residues	96
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	50.7 Å
Rg (real space) rg_real	14.68 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	2.7560e+06
I(0) uncertainty (real space) i0_real_error	3.0640e+04
Rg (reciprocal space) rg_reciprocal	14.69 Å
I(0) (reciprocal space) i0_reciprocal	2756000.0000
Solution quality estimate total_estimate	0.7864
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.119
Kurtosis Kurtosis kurtosis	-0.345
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	494800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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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	CRK-II SH2 domain
Molecular weight formula_weight	11328.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	981

DSEERSSWYWGRLSRQEAVALLQGQRHGVFLVRDSSTSPGDYVLSVSENSRVSHYIINSSGPRRLRIGDQEFDSLPALLEFYKIHYLDTTTLIEPVARS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	168

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5jn0a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

CATH v4.4 (1 domains)

Domain ID domain_id	5jn0A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

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8. Citations (1)

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Unit-cell length a length_a	86.082 Å
Unit-cell length b length_b	86.082 Å
Unit-cell length c length_c	33.847 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.677 Å
Low-resolution limit resolution_low	30.819 Å
R factor r_factor	0.1713
R_work r_work	0.1695
R_free r_free	0.2098

fit	/app/data/saxs_computation/jn/5jn0/5jn0.fit
pddf	/app/data/pr_computation/jn/5jn0/5jn0.pr.out
profile	/app/data/saxs_computation/jn/5jn0/5jn0.dat

CRK-II SH2 domain

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

CRK-II SH2 domain

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)