SAXSdb — 5dzd

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

E3 ubiquitin-protein ligase Itchy homolog

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Thioredoxin-interacting protein × 2 （Q9H3M7） UNKNOWN ATOM OR ION × 17 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ITCH_HUMAN
Isoform	Q96J02-3
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–47； UniProt 324–363 Author chain B； PDBConstruct 8–47； UniProt 324–363

Thioredoxin-interacting protein

OrganismNot specified

UniProt Q9H3M7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	E3 ubiquitin-protein ligase Itchy homolog × 2 （Q96J02） UNKNOWN ATOM OR ION × 17 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TXNIP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–13； UniProt 327–338 Author chain D； PDBConstruct 2–13； UniProt 327–338

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	5dzd
Deposition date deposition_date	2015-09-25
Structure title title	Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide
Keywords keywords	structural genomics, Structural Genomics Consortium, SGC, LIGASE-PROTEIN BINDING complex; LIGASE/PROTEIN BINDING
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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dzd__assembly_1__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase Itchy homolog
Molecular weight formula_weight	5503.2 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,B
Atom count atom_count	897

GRRASVELNEKPLPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKS

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	Thioredoxin-interacting protein
Molecular weight formula_weight	1359.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

XTPEAPPCYMDVIX

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	17

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

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Unit-cell length a length_a	52.668 Å
Unit-cell length b length_b	52.668 Å
Unit-cell length c length_c	82.476 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.570 Å
Low-resolution limit resolution_low	37.240 Å
R factor r_factor	0.1760
R_work r_work	0.1750
R_free r_free	0.2060

Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide

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

E3 ubiquitin-protein ligase Itchy homolog

State in the Current Structure

Other States of the Same Protein in the Database

Thioredoxin-interacting protein

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

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 water

7. Citations (1)

Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide

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

E3 ubiquitin-protein ligase Itchy homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Thioredoxin-interacting protein

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

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 water

7. Citations (1)