SAXSdb — 3hwj

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

E3 ubiquitin-protein ligase MYCBP2

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	DIMETHYL SULFOXIDE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	DIMETHYL SULFOXIDE × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MYCB2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–164； UniProt 1685–1845 Author chain B； PDBConstruct 4–164； UniProt 1685–1845

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	3hwj
Deposition date deposition_date	2009-06-17
Structure title title	Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)
Keywords keywords	;Myc-binding protein 2, MYCBP2, PHR proteins, PHR domain, Probable E3 ubiquitin-protein ligase MYCBP2, Protein Associated with Myc, PAM, Phr1, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM, NYSGXRC, Alternative splicing, Ligase, Metal-binding, Nucleus, Phosphoprotein, Transcription, Transcription regulation, Ubl conjugation pathway, Zinc, Zinc-finger, New York SGX Research Center for Structural Genomics ;; 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.

3hwj__assembly_1__model_1

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

Download this curve (.dat)

3hwj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hwj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.60 Å
Rg (electron density)	14.28 Å
Total Rg	15.45 Å
Atom count	1133
Residues	148
Excluded volume	19978 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hwj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3hwj__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 MYCBP2
Molecular weight formula_weight	18973.5 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	2447

MSLNRFTKTSQGRSWNTGNGSPDAICFAVDKPGIVVVGFAVYGGGGIHEYELEVLVDDSEHAGDSTHSHRWTSLELVKGTYTTDDSPSDIAEIRLDKVVPLKENVKYAVRLRNYGSRTANGDGGMTTVQCPDGVTFTFSTCSLSSNGTNQTRGQIPQILYYRSEEGHHHHHH

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3hwjA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	820 — PHR domain

Domain ID domain_id	3hwjB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	820 — PHR domain

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Unit-cell length a length_a	93.877 Å
Unit-cell length b length_b	99.922 Å
Unit-cell length c length_c	83.054 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	31.940 Å
R factor r_factor	0.2010
R_work r_work	0.1980
R_free r_free	0.2560

Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)

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

E3 ubiquitin-protein ligase MYCBP2

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

3hwj__assembly_1__model_1

3hwj__assembly_1__model_1 | I(q)

3hwj__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)

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

E3 ubiquitin-protein ligase MYCBP2

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

3hwj__assembly_1__model_1

3hwj__assembly_1__model_1 | I(q)

3hwj__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)