SAXSdb — 5xve

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

Ubiquitin carboxyl-terminal hydrolase 2

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	Ubiquitin-40S ribosomal protein S27a × 1 （P62992） ZINC ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–348； UniProt 258–605

Ubiquitin-40S ribosomal protein S27a

OrganismNot specified

UniProt P62992

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 2 × 1 （O75604） ZINC ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS27A_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76

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	5xve
Deposition date deposition_date	2017-06-27
Structure title title	Crystal structure of human USP2 C276S mutant in complex with ubiquitin
Keywords keywords	ubiquitin specific protease for anticancer target, HYDROLASE; HYDROLASE
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.

5xve__assembly_1__model_1

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

Download this curve (.dat)

5xve__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xve__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.37 Å
Rg (electron density)	20.90 Å
Total Rg	21.95 Å
Atom count	3285
Residues	407
Excluded volume	58156 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xve__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 (4)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 2
Molecular weight formula_weight	41193.6 kDa
EC 编号 ec_number	3.4.19.12
Mutation mutation	C276S
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	3761

MNSKSAQGLAGLRNLGNTSFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPSRMLEHHHHHH

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	Ubiquitin-40S ribosomal protein S27a
Molecular weight formula_weight	8576.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	356

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5xvea_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.9 — Ubiquitin carboxyl-terminal hydrolase, UCH

Domain ID domain_id	d5xveb_
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	5xveA00
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	102.473 Å
Unit-cell length b length_b	54.011 Å
Unit-cell length c length_c	74.753 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.240 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1478
R_work r_work	0.1469
R_free r_free	0.1640

Crystal structure of human USP2 C276S mutant in complex with ubiquitin

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

Ubiquitin carboxyl-terminal hydrolase 2

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-40S ribosomal protein S27a

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

5xve__assembly_1__model_1

5xve__assembly_1__model_1 | I(q)

5xve__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of human USP2 C276S mutant in complex with ubiquitin

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

Ubiquitin carboxyl-terminal hydrolase 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

Ubiquitin-40S ribosomal protein S27a

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

5xve__assembly_1__model_1

5xve__assembly_1__model_1 | I(q)

5xve__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)