SAXSdb — 5ohp

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

Ubiquitin carboxyl-terminal hydrolase 30

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	Polyubiquitin-B × 2 （P0CG47） ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP30_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–117； UniProt 64–178 Author chain A； PDBConstruct 122–262； UniProt 217–357 Author chain A； PDBConstruct 266–336； UniProt 432–502

Polyubiquitin-B

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin carboxyl-terminal hydrolase 30 × 1 （Q70CQ3） ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain C； 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	5ohp
Deposition date deposition_date	2017-07-17
Structure title title	Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin
Keywords keywords	DUB, Ubiquitin, USP, K6, 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.

5ohp__assembly_1__model_1

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

Download this curve (.dat)

5ohp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ohp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.37 Å
Rg (electron density)	23.17 Å
Total Rg	24.12 Å
Atom count	3679
Residues	465
Excluded volume	65242 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 30
Molecular weight formula_weight	38437.4 kDa
EC 编号 ec_number	3.4.19.12,3.4.19.12,3.4.19.12
Mutation mutation	construct 13i (C77A, R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A)
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	3731

GPKGLVPGLVNLGNTAFMNSLLQGLSACPAFIRWLEEFTSQYSRDQKEPPSHQYLSLTLLHLLKALSCQEVTDDEVLDASCLLDVLRMYRWQISSFEEQDAHELFHVITSSLEDERDGSGSHWKSQHPFHGRLTSNMVCKHCEHQSPVRFDTFDSLSLSIPAATWGHPLTLDHCLHHFISSESVRDVVCDNCTKIEAKGTLNGEKVEHQRTTFVKQLKLGKLPQCLCIHLQRLSWSSHGTPLKRHEHVQFNEDLSMDEYKYHSNASTYLFRLMAVVVHHGDMHSGHFVTYRRSPPSARNPLSTSNQWLWVSDDTVRKASLQEVLSSSAYLLFYERV

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	Polyubiquitin-B
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
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	52

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5ohpa_
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.3.1.0 — automated matches

Domain ID domain_id	d5ohpb_
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	d5ohpc_
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	5ohpA01
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	117.504 Å
Unit-cell length b length_b	117.504 Å
Unit-cell length c length_c	138.842 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	82.077 Å
R factor r_factor	0.2176
R_work r_work	0.2158
R_free r_free	0.2494

Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin

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

Ubiquitin carboxyl-terminal hydrolase 30

State in the Current Structure

Other States of the Same Protein in the Database

Polyubiquitin-B

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

5ohp__assembly_1__model_1

5ohp__assembly_1__model_1 | I(q)

5ohp__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin

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

Ubiquitin carboxyl-terminal hydrolase 30

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polyubiquitin-B

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

5ohp__assembly_1__model_1

5ohp__assembly_1__model_1 | I(q)

5ohp__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

7. Citations (1)