SAXSdb — 5c7m

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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 2	Polyubiquitin-C × 1 （P0CG48） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ITCH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–394； UniProt 524–899

Polyubiquitin-C

Homo sapiens

UniProt P0CG48

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 Itchy homolog × 1 （Q96J02） water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–75； UniProt 1–75 Author chain C； PDBConstruct 1–75； UniProt 1–75

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	5c7m
Deposition date deposition_date	2015-06-24
Structure title title	CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT
Keywords keywords	;LIGASE, UBIQUITIN-PROTEIN LIGASE, UBIQUITIN VARIANT, Structural Genomics Consortium, SGC, Structural Genomics, LIGASE-SIGNALING PROTEIN complex ;; LIGASE/SIGNALING PROTEIN
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.

5c7m__assembly_1__model_1

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

Download this curve (.dat)

5c7m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5c7m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.35 Å
Rg (electron density)	24.29 Å
Total Rg	25.12 Å
Atom count	3294
Residues	441
Excluded volume	57603 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5c7m__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5c7m__assembly_2__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase Itchy homolog
Molecular weight formula_weight	47028.7 kDa
EC 编号 ec_number	6.3.2.-
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	3871

MHHHHHHSSGRENLYFQGYVRDFKAKVQYFRFWCQQLAMPQHIKITVTRKTLFEDSFQQIMSFSPQDLRRRLWVIFPGEEGLDYGGVAREWFFLLSHEVSNPMYCLFEYAGKDNYCLQINPASYINPDHLKYFRFIGRFIAMALFHGKFIDTGFSLPFYKRILNKPVGLKDLESIDPEFYNSLIWVKENNIEECDLEMYFSVDKEILGEIKSHDLKPNGGNILVTEENKEEYIRMVAEWRLSRGVEEQTQAFFEGFNEILPQQYLQYFDAKELEVLLCGMQEIDLNDWQRHAIYRRYARTSKQIMWFWQFVKEIDNEKRMRLLQFVTGTCRLPVGGFADLMGSNGPQKFCIEKVGKENWLPRSHTCFNRLDLPPYKSYEQLKEKLLFAIEETEG

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	Polyubiquitin-C
Molecular weight formula_weight	9768.2 kDa
Mutation mutation	Q2H, F3L, T9R, I44L, A46G, K48N, Q49K, T66N, H68Y, V70L, L73R, R74L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MHILVKTLRGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLLFGGNKLEDGRTLSDYNIQKESNLYLLLRRLGSKFHHHHHH

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5c7ma_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.148 — Hect, E3 ligase catalytic domain
Superfamily Superfamily superfamily	d.148.1 — Hect, E3 ligase catalytic domain
Family Family family	d.148.1.0 — automated matches

Domain ID domain_id	d5c7mb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d5c7mc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

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Unit-cell length a length_a	121.115 Å
Unit-cell length b length_b	121.115 Å
Unit-cell length c length_c	85.547 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 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	3.030 Å
Low-resolution limit resolution_low	49.430 Å
R factor r_factor	0.2554
R_work r_work	0.2537
R_free r_free	0.2969

CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT

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

Polyubiquitin-C

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

5c7m__assembly_1__model_1

5c7m__assembly_1__model_1 | I(q)

5c7m__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT

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

Polyubiquitin-C

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

5c7m__assembly_1__model_1

5c7m__assembly_1__model_1 | I(q)

5c7m__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)