SAXSdb — 9ye9

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

Ubiquitin-conjugating enzyme E2 D2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	E3 ubiquitin-protein ligase CHIP × 2 （F6NGW2） BETA-MERCAPTOETHANOL × 5 CHLORIDE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UB2D2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–152； UniProt 1–147

E3 ubiquitin-protein ligase CHIP

Danio rerio

UniProt F6NGW2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） BETA-MERCAPTOETHANOL × 5 CHLORIDE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F6NGW2_DANRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–86； UniProt 204–284 Author chain C； PDBConstruct 6–86； UniProt 204–284

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	9ye9
Deposition date deposition_date	2025-09-23
Structure title title	Structure of UbcH5b in complex with the U-box domain of the E3 ubiquitin ligase CHIP
Keywords keywords	Ubiquitin conjugating enzyme, ubiquitin ligase, LIGASE; LIGASE
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.

9ye9__assembly_1__model_1

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

Download this curve (.dat)

9ye9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ye9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.98 Å
Rg (electron density)	24.29 Å
Total Rg	25.01 Å
Atom count	2352
Residues	294
Excluded volume	42023 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ye9__assembly_1__model_1`	trimeric （3）	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	Ubiquitin-conjugating enzyme E2 D2
Molecular weight formula_weight	17182.7 kDa
EC 编号 ec_number	2.3.2.23,2.3.2.24
Mutation mutation	M1K, C85K
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	2495

GAMGSKALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM

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	E3 ubiquitin-protein ligase CHIP
Molecular weight formula_weight	9894.2 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAMGSKKREIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAMKEVIDAFIQENGWVEDY

Source Source

Source organism organism	Danio rerio
Common name common_name	zebrafish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	143

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Unit-cell length a length_a	58.081 Å
Unit-cell length b length_b	59.138 Å
Unit-cell length c length_c	112.834 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	8

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

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	41.440 Å
R factor r_factor	0.2450
R_work r_work	0.2415
R_free r_free	0.2881

Structure of UbcH5b in complex with the U-box domain of the E3 ubiquitin ligase CHIP

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

Ubiquitin-conjugating enzyme E2 D2

State in the Current Structure

Other States of the Same Protein in the Database

E3 ubiquitin-protein ligase CHIP

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

9ye9__assembly_1__model_1

9ye9__assembly_1__model_1 | I(q)

9ye9__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Structure of UbcH5b in complex with the U-box domain of the E3 ubiquitin ligase CHIP

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

Ubiquitin-conjugating enzyme E2 D2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E3 ubiquitin-protein ligase CHIP

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

9ye9__assembly_1__model_1

9ye9__assembly_1__model_1 | I(q)

9ye9__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)