SAXSdb — 3wxe

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

Uncharacterized protein

Danio rerio

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin × 1 （P0CG48） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E7FEV5_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–206； UniProt 578–780 Author chain A； PDBConstruct 211–312； UniProt 850–951

Ubiquitin

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	Uncharacterized protein × 1 （E7FEV5） water × 2	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 1–148； UniProt 1–148

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	3wxe
Deposition date deposition_date	2014-07-30
Structure title title	Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin
Keywords keywords	ubiquitin protease, HYDROLASE-PROTEIN BINDING complex; HYDROLASE/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.

3wxe__assembly_1__model_1

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

Download this curve (.dat)

3wxe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wxe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.45 Å
Rg (electron density)	22.21 Å
Total Rg	23.20 Å
Atom count	3617
Residues	449
Excluded volume	65024 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wxe__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	35991.5 kDa
Mutation mutation	C596S, B-box deletion
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	3664

SHMGLEVMVGKKKGIQGHYNSSYLDSTLFCLFSFSSVLDTVLLRPRSKTDVEYYKETQELLRTEIVNPLRIHGYVCATKIMKLRRILEKVEAASGFTSEEKDPEEFLNILFHHILRVDPLLRLRSAGQKVQDCYFYQIFMDKKDKVMVPTSQQLLEWSFINSDLKFAEAPSCLIIQMPRFGKDFKMFNKIFPSLELDITDLLDDTPLEGGPHQQMELFAVLCIETSHYVAFVKYGSADSAWLFFDSMADRDGGQNGFNIPQVSRCPEVGEYLKMTPEELHALDPKNIQGYARRLLCDAYMCMYQSPTMSLYK

Source Source

Source organism organism	Danio rerio
Common name common_name	zebra fish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	16751.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR

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	47

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3wxeb1
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	d3wxeb2
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

CATH v4.4 (1 domains)

Domain ID domain_id	3wxeA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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Unit-cell length a length_a	64.676 Å
Unit-cell length b length_b	49.788 Å
Unit-cell length c length_c	71.003 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1852
R_work r_work	0.1819
R_free r_free	0.2472

Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin

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

Uncharacterized protein

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin

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

3wxe__assembly_1__model_1

3wxe__assembly_1__model_1 | I(q)

3wxe__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 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin

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

Uncharacterized 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

Ubiquitin

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

3wxe__assembly_1__model_1

3wxe__assembly_1__model_1 | I(q)

3wxe__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 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)