SAXSdb — 2y1n

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

E3 UBIQUITIN-PROTEIN LIGASE

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	TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE × 1 （P43403） ZINC ION × 2 CALCIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE × 1 （P43403） ZINC ION × 2 CALCIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBL_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–389； UniProt 47–435 Author chain C； PDBConstruct 1–389； UniProt 47–435

TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE

OrganismNot specified

UniProt P43403

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	E3 UBIQUITIN-PROTEIN LIGASE × 1 （P22681） ZINC ION × 2 CALCIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	E3 UBIQUITIN-PROTEIN LIGASE × 1 （P22681） ZINC ION × 2 CALCIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZAP70_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–12； UniProt 286–297 Author chain D； PDBConstruct 1–12； UniProt 286–297

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	2y1n
Deposition date deposition_date	2010-12-08
Structure title title	Structure of c-Cbl-ZAP-70 peptide complex
Keywords keywords	LIGASE-TRANSFERASE COMPLEX, UBIQUITIN RING E3 LIGASE; LIGASE/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.

2y1n__assembly_1__model_1

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

Download this curve (.dat)

2y1n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y1n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.80 Å
Rg (electron density)	21.52 Å
Total Rg	22.45 Å
Atom count	3154
Residues	388
Excluded volume	56418 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y1n__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2y1n__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	E3 UBIQUITIN-PROTEIN LIGASE
Molecular weight formula_weight	44928.7 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6623

PPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTGLCEPTPQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPFD

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

Entity 2 Entity 2 polymer

Description description	TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
Molecular weight formula_weight	1344.3 kDa
EC 编号 ec_number	2.7.10.2
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

TLNSDGYTPEPA

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	340

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2y1nA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	20 — Adaptor protein Cbl, N-terminal domain

Domain ID domain_id	2y1nA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2y1nA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	2y1nA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	2y1nC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	20 — Adaptor protein Cbl, N-terminal domain

Domain ID domain_id	2y1nC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2y1nC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	2y1nC04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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Unit-cell length a length_a	93.570 Å
Unit-cell length b length_b	93.570 Å
Unit-cell length c length_c	189.599 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	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.999 Å
Low-resolution limit resolution_low	45.423 Å
R factor r_factor	0.1590
R_work r_work	0.1582
R_free r_free	0.1804

Structure of c-Cbl-ZAP-70 peptide complex

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

E3 UBIQUITIN-PROTEIN LIGASE

State in the Current Structure

Other States of the Same Protein in the Database

TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE

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

2y1n__assembly_1__model_1

2y1n__assembly_1__model_1 | I(q)

2y1n__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Structure of c-Cbl-ZAP-70 peptide complex

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

E3 UBIQUITIN-PROTEIN LIGASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE

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

2y1n__assembly_1__model_1

2y1n__assembly_1__model_1 | I(q)

2y1n__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)