SAXSdb — 1skj

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

PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN

Rous sarcoma virus

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 142–252	Fragment：SH2 DOMAIN Mutation：N-TERMINAL INS(GS) AND C-TERMINAL INS(EFIVTD)	UR2 4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；20% PEG 6K, 0.1M ODIUM CACODYLATE PH 6, HANGING DROP EXPERIMENT, PROTEIN 29 MG/ ML, INHIBITOR 4 MG/ML, 4:4:2 RATIO (WELL:PROT:INHIB), pH 6.0, vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.275

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 1SKJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BKL SELF-ASSOCIATED APO SRC SH2 DOMAIN Deposited 1997-05-02	Different construct Different mutation/modification 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 145–249（105 aa） Fragment：SH2 DOMAIN	Mutation：INS(GS) AT N-TERMINUS, INS(EFIVTD) AT C-TERMINUS, BYPRODUCT OF CLONING	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；2M AMMONIUM SULFATE PH 6.6 , 25 MG/ML SRC SH2, SITTING DROPS, vapor diffusion - sitting drop	Resolution 2.10 Å R-free 0.304
1BKM COCRYSTAL STRUCTURE OF D-AMINO ACID SUBSTITUTED PHOSPHOPEPTIDE COMPLEX Deposited 1997-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 145–249（105 aa） Fragment：DOMAIN	Mutation：INS(G0,S1), INS(EFIVTD) AT C-TERMINUS	1C5 [[O-PHOSPHONO-N-ACETYL-TYROSINYL]-GLUTAMYL-3[CYCLOHEXYLMETHYL]ALANINYL]-AMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；5% PEG 6K, 0.1M TRIS, PH 8, SITTING DROP EXPERIMENT, PROTEIN 50 MG/ML, INHIBITOR 4 MG/ML, 4:4:2 RATIO (WELL:PROT:INHIB), pH 8.0, vapor diffusion - sitting drop	Resolution 2.00 Å R-free 0.275
1IS0 Crystal Structure of a Complex of the Src SH2 Domain with Conformationally Constrained Peptide Inhibitor Deposited 2001-11-02	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 144–249（106 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；53% MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.272
1IS0 Crystal Structure of a Complex of the Src SH2 Domain with Conformationally Constrained Peptide Inhibitor Deposited 2001-11-02	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 B 144–249（106 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；53% MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.272
1KC2 structure of the triple (Lys(beta)D3Ala, Asp(beta)C8Ala, AspCD2Ala) mutant of the Src SH2 domain bound to the PQpYEEIPI peptide Deposited 2001-11-07	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 145–247（103 aa） Fragment：SH2 domain	Mutation：D190A, D192A, K200A	CO COBALT (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.267
1NZL Crystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYEpYIPI Deposited 2003-02-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 145–247（103 aa） Fragment：SH2 domain	Not recorded	CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；296 K；PEG 4000,magnesium chloride, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.90 Å R-free 0.265
1NZL Crystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYEpYIPI Deposited 2003-02-18	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 B 145–247（103 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；296 K；PEG 4000,magnesium chloride, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.90 Å R-free 0.265
1NZV Crystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYIpYVPA Deposited 2003-02-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 145–247（103 aa） Fragment：SH2 domain	Not recorded	CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；296 K；PEG 4000, magnesium chloride,Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.271
1NZV Crystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYIpYVPA Deposited 2003-02-19	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 B 145–247（103 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；296 K；PEG 4000, magnesium chloride,Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.271
1SHA CRYSTAL STRUCTURE OF THE PHOSPHOTYROSINE RECOGNITION DOMAIN SH2 OF V-SRC COMPLEXED WITH TYROSINE-PHOSPHORYLATED PEPTIDES Deposited 1992-08-18	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 143–246（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å
1SHB CRYSTAL STRUCTURE OF THE PHOSPHOTYROSINE RECOGNITION DOMAIN SH2 OF V-SRC COMPLEXED WITH TYROSINE-PHOSPHORYLATED PEPTIDES Deposited 1992-08-18	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 143–246（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1SPR BINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 DOMAIN: CRYSTAL STRUCTURES OF THE COMPLEXED AND PEPTIDE-FREE FORMS Deposited 1993-03-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 144–247（104 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1SPR BINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 DOMAIN: CRYSTAL STRUCTURES OF THE COMPLEXED AND PEPTIDE-FREE FORMS Deposited 1993-03-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 144–247（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1SPR BINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 DOMAIN: CRYSTAL STRUCTURES OF THE COMPLEXED AND PEPTIDE-FREE FORMS Deposited 1993-03-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 144–247（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1SPR BINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 DOMAIN: CRYSTAL STRUCTURES OF THE COMPLEXED AND PEPTIDE-FREE FORMS Deposited 1993-03-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 144–247（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1SPS BINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 DOMAIN: CRYSTAL STRUCTURES OF THE COMPLEXED AND PEPTIDE-FREE FORMS Deposited 1993-03-05	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 144–247（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
1SPS BINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 DOMAIN: CRYSTAL STRUCTURES OF THE COMPLEXED AND PEPTIDE-FREE FORMS Deposited 1993-03-05	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 B 144–247（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
1SPS BINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 DOMAIN: CRYSTAL STRUCTURES OF THE COMPLEXED AND PEPTIDE-FREE FORMS Deposited 1993-03-05	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 C 144–247（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å

10 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SRC_RSVSA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–112； UniProt 142–252

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	1skj
Deposition date deposition_date	1997-09-18
Structure title title	COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX
Keywords keywords	TYROSINE-PROTEIN KINASE, V-SRC SH2 DOMAIN, PHOSPHOTYROSINE RECOGNITION DOMAIN, PP60 SRC SH2 DOMAIN, PEPTIDOMIMETIC, UREIDO; TYROSINE-PROTEIN KINASE
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	14.55 Å
Radius of gyration Rg (electron density) rg_electron	13.17 Å
Forward intensity I(0) i0	3095530.00
Molecular weight molecular_weight	12182.0 kDa
Excluded volume excluded_volume	15190 Å³
Envelope volume envelope_volume	16748 Å³
Hydration-shell volume shell_volume	10979 Å³
Envelope diameter envelope_diameter	50.1 Å
Shell Rg shell_rg	18.84 Å
Envelope Rg envelope_rg	13.55 Å
Shape Rg shape_rg	13.16 Å
Total Rg total_rg	14.43 Å
Total atoms total_atoms	1095
Residues n_residues	102
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	49.9 Å
Rg (real space) rg_real	14.48 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	3.0960e+06
I(0) uncertainty (real space) i0_real_error	3.5010e+04
Rg (reciprocal space) rg_reciprocal	14.49 Å
I(0) (reciprocal space) i0_reciprocal	3096000.0000
Solution quality estimate total_estimate	0.8608
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.226
Kurtosis Kurtosis kurtosis	-0.172
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	498100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.735; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.987

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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	PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN
Molecular weight formula_weight	12907.5 kDa
EC 编号 ec_number	2.7.1.112
Mutation mutation	N-TERMINAL INS(GS) AND C-TERMINAL INS(EFIVTD)
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	1278

GSAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPTSKEFIVTD

来源 Source

来源生物 organism	Rous sarcoma virus
NCBI Class编号 ncbi_taxonomy_id	11886
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID
Molecular weight formula_weight	571.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1skja_
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	1skjA00
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 (2)

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Unit-cell length a length_a	74.400 Å
Unit-cell length b length_b	74.400 Å
Unit-cell length c length_c	38.800 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 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2750

fit	/app/data/saxs_computation/sk/1skj/1skj.fit
pddf	/app/data/pr_computation/sk/1skj/1skj.pr.out
profile	/app/data/saxs_computation/sk/1skj/1skj.dat

COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX

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

PP60 V-SRC TYROSINE KINASE TRANSFORMING 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