SAXSdb — 7q5u

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

Tyrosine-protein kinase SYK

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） 1,2-ETHANEDIOL × 2 DI(HYDROXYETHYL)ETHER × 1 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） DI(HYDROXYETHYL)ETHER × 1 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KSYK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 2–265； UniProt 6–269 Author chain BBB； PDBConstruct 2–265； UniProt 6–269 Author chain CCC； PDBConstruct 2–265； UniProt 6–269 Author chain DDD； PDBConstruct 2–265； UniProt 6–269 Author chain EEE； PDBConstruct 2–265； UniProt 6–269 Author chain FFF； PDBConstruct 2–265； UniProt 6–269

T-cell surface glycoprotein CD3 gamma chain

OrganismNot specified

UniProt P09693

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein kinase SYK × 1 （P43405） 1,2-ETHANEDIOL × 2 DI(HYDROXYETHYL)ETHER × 1 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein kinase SYK × 1 （P43405） DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein kinase SYK × 1 （P43405） 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein kinase SYK × 1 （P43405） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein kinase SYK × 1 （P43405） DI(HYDROXYETHYL)ETHER × 1 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein kinase SYK × 1 （P43405） DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD3G_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain GGG； PDBConstruct 1–20； UniProt 157–176 Author chain HHH； PDBConstruct 1–20； UniProt 157–176 Author chain III； PDBConstruct 1–20； UniProt 157–176 Author chain JJJ； PDBConstruct 1–20； UniProt 157–176 Author chain KKK； PDBConstruct 1–20； UniProt 157–176 Author chain LLL； PDBConstruct 1–20； UniProt 157–176

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	7q5u
Deposition date deposition_date	2021-11-04
Structure title title	The tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide
Keywords keywords	Signalling, kinase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7q5u__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7q5u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7q5u__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.37 Å
Rg (electron density)	20.42 Å
Total Rg	21.36 Å
Atom count	2258
Residues	275
Excluded volume	40023 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7q5u__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7q5u__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7q5u__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7q5u__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`7q5u__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`7q5u__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein kinase SYK
Molecular weight formula_weight	29907.0 kDa
EC 编号 ec_number	2.7.10.2
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,BBB,CCC,DDD,EEE,FFF
Atom count atom_count	14063

SMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRNYLGGFALSVAHGRKAHHYTIERELNGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRPQGVQPKTGPFEDLKENLIREYVKQTWNLQGQALEQAIISQKPQLEKLIATTAHEKMPWFHGKISREESEQIVLIGSKTNGKFLIRARDNNGSYALCLLHEGKVLHYRIDKDKTGKLSIPEGKKFDTLWQLVEHYSYKADGLLRVLTVPCQKIGTQGNVN

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	T-cell surface glycoprotein CD3 gamma chain
Molecular weight formula_weight	2611.5 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	GGG,HHH,III,JJJ,KKK,LLL

DQLYQPLKDREDDQYSHLQG

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 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	613

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Unit-cell length a length_a	92.321 Å
Unit-cell length b length_b	129.312 Å
Unit-cell length c length_c	95.346 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	93.830 Å
R factor r_factor	—
R_work r_work	0.2165
R_free r_free	0.2588

The tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide

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

Tyrosine-protein kinase SYK

State in the Current Structure

Other States of the Same Protein in the Database

T-cell surface glycoprotein CD3 gamma chain

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7q5u__assembly_1__model_1

7q5u__assembly_1__model_1 | I(q)

7q5u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source 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. Citations (1)

The tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide

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

Tyrosine-protein kinase SYK

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T-cell surface glycoprotein CD3 gamma chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7q5u__assembly_1__model_1

7q5u__assembly_1__model_1 | I(q)

7q5u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source 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. Citations (1)