SAXSdb — 12zj

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

Ubiquitin carboxyl-terminal hydrolase 7

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	MAGE-like protein 2 × 1 （Q9UJ55） MAGNESIUM ION × 2 GLYCEROL × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	MAGE-like protein 2 × 1 （Q9UJ55） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	MAGE-like protein 2 × 1 （Q9UJ55） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–145； UniProt 62–205 Author chain C； PDBConstruct 2–145； UniProt 62–205 Author chain E； PDBConstruct 2–145； UniProt 62–205

MAGE-like protein 2

OrganismNot specified

UniProt Q9UJ55

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 7 × 1 （Q93009） MAGNESIUM ION × 2 GLYCEROL × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 7 × 1 （Q93009） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 7 × 1 （Q93009） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MAGL2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–13； UniProt 968–980 Author chain D； PDBConstruct 1–13； UniProt 968–980 Author chain F； PDBConstruct 1–13； UniProt 968–980

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	12zj
Deposition date deposition_date	2026-04-24
Last revision last_revision	2026-06-10
Structure title title	Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)
Keywords keywords	Deubiquitinase TRAF domain Complex Ubiquitin signaling, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING 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.

12zj__assembly_1__model_1

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

Download this curve (.dat)

12zj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

12zj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.14 Å
Rg (electron density)	15.87 Å
Total Rg	16.84 Å
Atom count	1283
Residues	153
Excluded volume	22563 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`12zj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`12zj__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`12zj__assembly_3__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	Ubiquitin carboxyl-terminal hydrolase 7
Molecular weight formula_weight	16987.0 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	4306

GDTSWRSEATFQFTVERFSRLSESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQCNAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPHGVAW

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	MAGE-like protein 2
Molecular weight formula_weight	1319.4 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

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

SAWEGPSTSRALG

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	472

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Unit-cell length a length_a	57.483 Å
Unit-cell length b length_b	50.696 Å
Unit-cell length c length_c	82.974 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.630 Å
Low-resolution limit resolution_low	41.500 Å
R factor r_factor	0.1950
R_work r_work	0.1940
R_free r_free	0.2170

Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)

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

Ubiquitin carboxyl-terminal hydrolase 7

State in the Current Structure

Other States of the Same Protein in the Database

MAGE-like protein 2

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

12zj__assembly_1__model_1

12zj__assembly_1__model_1 | I(q)

12zj__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

7. Citations (1)

Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)

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

Ubiquitin carboxyl-terminal hydrolase 7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

MAGE-like protein 2

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

12zj__assembly_1__model_1

12zj__assembly_1__model_1 | I(q)

12zj__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

7. Citations (1)