SAXSdb — 2ydl

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

SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1

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 270–328	Fragment：SH3 C, RESIDUES 270-328	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：0.1M CITRATE PH 5.5, 2.0 M AMMONIUM SULPHATE	Resolution 2.05 Å R-free 0.252

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 2YDL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BZ8 N-terminal Sh3 domain of CIN85 bound to Cbl-b peptide Deposited 2005-08-12	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 A 1–58（58 aa） Fragment：N-TERMINAL SH3 DOMAIN RESIDUES 1-58 Chain B 1–58（58 aa） Fragment：N-TERMINAL SH3 DOMAIN RESIDUES 1-58	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.8 M NA CITRATE, 0.1 M BIS-TRIS PH 7.5, 0.2 M NACL	Resolution 2.00 Å R-free 0.271
2K6D CIN85 Sh3-C domain in complex with ubiquitin Deposited 2008-07-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 267–328（62 aa） Fragment：CIN85 SH3-C domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 0.150；Pressure ambient NMR sample composition 0.1 mM CIN85, 0.1 mM [U-100% 15N] ubiquitin, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.1 mM [U-100% 15N] CIN85, 0.1 mM ubiquitiny, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] CIN85, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K9G Solution structure of the third SH3 domain of the Cin85 adapter protein Deposited 2008-10-10	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 262–333（72 aa） Fragment：SH3 domain C, UNP residues 262-333	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 140；Pressure ambient NMR sample composition 1mM Cin85 SH3-C, 20mM sodium phosphate, 100mM sodium chloride, 1mM DTT, 1mM EDTA, 0.02% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM [U-98% 13C; U-98% 15N] Cin85 SH3-C, 20mM sodium phosphate, 100mM sodium chloride, 1mM DTT, 1mM EDTA, 0.02% sodium azide, 100% D2O \| 100% D2O NMR sample composition 1mM [U-99% 15N] Cin85 SH3-C, 20mM sodium phosphate, 100mM sodium chloride, 1mM DTT, 1mM EDTA, 0.02% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM [U-99% 13C; U-99% 15N] Cin85 SH3-C, 20mM sodium phosphate, 100mM sodium chloride, 1mM DTT, 1mM EDTA, 0.02% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N64 NMR Structure of the C-terminal Coiled-Coil Domain of CIN85 Deposited 2015-08-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 594–665（72 aa） Fragment：Coiled coil domain residues 594-665 Chain B 594–665（72 aa） Fragment：Coiled coil domain residues 594-665 Chain C 594–665（72 aa） Fragment：Coiled coil domain residues 594-665	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；305 K；Pressure ambient NMR sample composition 1-3 mM [U-13C; U-15N; U-2H] CIN85 CC-domain, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1-3 mM [U-13C; U-15N; U-2H] CIN85 CC-domain, 1-3 mM [U-2H] CIN85 CC-domain, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2O2O Solution structure of domain B from human CIN85 PROTEIN Deposited 2006-11-30	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–168（77 aa） Fragment：CIN85_B	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 20mM PO4, 100mM NACL, 1mM EDTA, 2mM DTT, 0.01% NAN3；Pressure AMBIENT NMR sample composition 1MM CIN85_B U-15N PHOSPHATE BUFFER; 1MM CIN85_B U-15N,13C; 20MM PHOSPHATE BUFFER; 1MM CIN85_B U-15N,13C; 20MM PHOSPHATE BUFFER	Resolution not provided
5ABS CRYSTAL STRUCTURE OF THE C-TERMINAL COILED-COIL DOMAIN OF CIN85 IN SPACE GROUP P321 Deposited 2015-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 599–662（64 aa） Fragment：COILED-COIL DOMAIN, RESIDUES 599-662	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.05M ZN ACETATE, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 7	Resolution 1.74 Å R-free 0.283

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SH3K1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–61； UniProt 270–328

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	2ydl
Deposition date deposition_date	2011-03-22
Structure title title	Crystal structure of SH3C from CIN85
Keywords keywords	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	13.67 Å
Radius of gyration Rg (electron density) rg_electron	12.27 Å
Forward intensity I(0) i0	1372960.00
Molecular weight molecular_weight	7725.0 kDa
Excluded volume excluded_volume	9629 Å³
Envelope volume envelope_volume	11607 Å³
Hydration-shell volume shell_volume	8575 Å³
Envelope diameter envelope_diameter	46.5 Å
Shell Rg shell_rg	17.27 Å
Envelope Rg envelope_rg	12.98 Å
Shape Rg shape_rg	12.31 Å
Total Rg total_rg	13.51 Å
Total atoms total_atoms	547
Residues n_residues	67
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	48.6 Å
Rg (real space) rg_real	13.70 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.3730e+06
I(0) uncertainty (real space) i0_real_error	1.5380e+04
Rg (reciprocal space) rg_reciprocal	13.70 Å
I(0) (reciprocal space) i0_reciprocal	1373000.0000
Solution quality estimate total_estimate	0.8307
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.0 Å
Skewness Skewness skewness	0.496
Kurtosis Kurtosis kurtosis	0.141
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	303500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.626; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.981

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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) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2ydla1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.0 — automated matches

Domain ID domain_id	d2ydla2
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	d2ydla3
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 (1 domains)

Domain ID domain_id	2ydlA00
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	47.828 Å
Unit-cell length b length_b	47.828 Å
Unit-cell length c length_c	70.235 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	41.420 Å
R factor r_factor	0.2074
R_work r_work	0.2051
R_free r_free	0.2522

Description description	SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1
Molecular weight formula_weight	8035.0 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	603

Crystal structure of SH3C from CIN85

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

SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1

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) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 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	56

fit	/app/data/saxs_computation/yd/2ydl/2ydl.fit
pddf	/app/data/pr_computation/yd/2ydl/2ydl.pr.out
profile	/app/data/saxs_computation/yd/2ydl/2ydl.dat