SAXSdb — 1u59

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

Tyrosine-protein kinase ZAP-70

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 327–606	Fragment：kinase domain	STU STAUROSPORINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 3350, DL-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.271

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 1U59	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M61 Crystal structure of the apo SH2 domains of ZAP-70 Deposited 2002-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–256（256 aa） Fragment：tandem SH2 domains (Residues 1-256)	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG3350, Sodium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.286
2OQ1 Tandem SH2 domains of ZAP-70 with 19-mer zeta1 peptide Deposited 2007-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3–256（254 aa） Fragment：residues 3-256	Non-standard monomer：Yes (specific site not provided by mmCIF)	PB LEAD (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；20%PEG 4000, 50mM sodium citrate,100 mM ammonium acetate, 20mM DTT, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.255
2OZO Autoinhibited intact human ZAP-70 Deposited 2007-02-26	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 1–606（606 aa） Fragment：Inactive ZAP-70 (residues 1-606)	Mutation：Y315F,Y319F,D461N	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.05 M NaSCN, 21% PEG3350, protein mixed with 9 mM n-decyl-beta-D-thiomaltopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
2Y1N Structure of c-Cbl-ZAP-70 peptide complex Deposited 2010-12-08	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 D 286–297（12 aa） Fragment：PEPTIDE, RESIDUES 286-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 18-20% (W/V) PEG 3350, 0.2 M AMMONIUM FORMATE	Resolution 2.00 Å R-free 0.180
2Y1N Structure of c-Cbl-ZAP-70 peptide complex Deposited 2010-12-08	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 286–297（12 aa） Fragment：PEPTIDE, RESIDUES 286-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 18-20% (W/V) PEG 3350, 0.2 M AMMONIUM FORMATE	Resolution 2.00 Å R-free 0.180
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14	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 B 286–297（12 aa） Fragment：RESIDUES 286-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE	Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 286–297（12 aa） Fragment：RESIDUES 286-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE	Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain J 286–297（12 aa） Fragment：RESIDUES 286-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE	Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 286–297（12 aa） Fragment：RESIDUES 286-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE	Resolution 2.21 Å R-free 0.211
4A4B Structure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex Deposited 2011-10-08	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 B 286–297（12 aa） Fragment：ZAP-70 PEPTIDE, RESIDUES 286-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；31-35% PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 0.2 M KCL, 50 MM HEPES, PH 7.5	Resolution 2.79 Å R-free 0.267
4A4C Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex Deposited 2011-10-08	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 B 286–297（12 aa） Fragment：ZAP-70 PEPTIDE, RESIDUES 286-297	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；50 MM HEPES, PH 7.5, 0.2 M KCL AND 31-35% (V/V) PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) AT 4 DEGREES CELSIUS.	Resolution 2.70 Å R-free 0.268
4K2R Structural basis for activation of ZAP-70 by phosphorylation of the SH2-kinase linker Deposited 2013-04-09	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 1–606（606 aa）	Mutation：D461N	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M Bis-Tris pH 6.5, 20% Polyethylene glycol monomethyl ether 5,000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.287
4XZ0 ZAP-70-tSH2:compound-A complex Deposited 2015-02-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–259（259 aa）	Not recorded	4N5 1-(3-{5-[(3-chlorobenzyl)sulfonyl]-1H-tetrazol-1-yl}phenyl)ethanone × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 3350, ammonium sulfate, TCEP	Resolution 2.00 Å R-free 0.245
4XZ1 ZAP-70-tSH2:Compound-B adduct Deposited 2015-02-03	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 1–259（259 aa）	Not recorded	4N6 2-[(7-chloro-4-nitro-2,1,3-benzoxadiazol-5-yl)amino]ethanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 6000, calcium chloride, MES, TCEP	Resolution 2.80 Å R-free 0.270
7SIY cCBL TKB domain in complex with pZAP70 peptide Deposited 2021-10-15	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 Z 292–296（5 aa） Fragment：Residues 292-296	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ammonium formate, 20% PEG3350	Resolution 1.48 Å R-free 0.221

11 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ZAP70_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–280； UniProt 327–606

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	1u59
Deposition date deposition_date	2004-07-27
Structure title title	Crystal Structure of the ZAP-70 Kinase Domain in Complex with Staurosporine
Keywords keywords	TRANSFERASE; TRANSFERASE
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	20.14 Å
Radius of gyration Rg (electron density) rg_electron	19.08 Å
Forward intensity I(0) i0	18596300.00
Molecular weight molecular_weight	32980.0 kDa
Excluded volume excluded_volume	41396 Å³
Envelope volume envelope_volume	47883 Å³
Hydration-shell volume shell_volume	20721 Å³
Envelope diameter envelope_diameter	65.4 Å
Shell Rg shell_rg	25.72 Å
Envelope Rg envelope_rg	19.42 Å
Shape Rg shape_rg	19.06 Å
Total Rg total_rg	20.07 Å
Total atoms total_atoms	2316
Residues n_residues	282
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	65.5 Å
Rg (real space) rg_real	20.04 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.8600e+07
I(0) uncertainty (real space) i0_real_error	2.3290e+05
Rg (reciprocal space) rg_reciprocal	20.06 Å
I(0) (reciprocal space) i0_reciprocal	18600000.0000
Solution quality estimate total_estimate	0.8923
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.199
Kurtosis Kurtosis kurtosis	-0.459
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	7342000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.995

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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	Tyrosine-protein kinase ZAP-70
Molecular weight formula_weight	33247.6 kDa
EC 编号 ec_number	2.7.1.112
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	2376

DKKLFLKRDNLLIADIELGCGNFGSVRQGVYRMRKKQIDVAIKVLKQGTEKADTEEMMREAQIMHQLDNPYIVRLIGVCQAEALMLVMEMAGGGPLHKFLVGKREEIPVSNVAELLHQVSMGMKYLEEKNFVHRDLAARNVLLVNRHYAKISDFGLSKALGADDSYYTARSAGKWPLKWYAPECINFRKFSSRSDVWSYGVTMWEALSYGQKPYKKMKGPEVMAFIEQGKRMECPPECPPELYALMSDCWIYKWEDRPDFLTVEQRMRACYYSLASKVEGHHHHHHH

来源 Source

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	STAUROSPORINE
Molecular weight formula_weight	466.5 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	54

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1u59a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d1u59a2
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	1u59A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	1u59A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	43.056 Å
Unit-cell length b length_b	57.064 Å
Unit-cell length c length_c	125.133 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.960 Å
R factor r_factor	—
R_work r_work	0.2170
R_free r_free	0.2710

fit	/app/data/saxs_computation/u5/1u59/1u59.fit
pddf	/app/data/pr_computation/u5/1u59/1u59.pr.out
profile	/app/data/saxs_computation/u5/1u59/1u59.dat

Crystal Structure of the ZAP-70 Kinase Domain in Complex with Staurosporine

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

Tyrosine-protein kinase ZAP-70

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