SAXSdb — 9e7k

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

Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5

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	Nb-cS1 × 1 Proteasomal ubiquitin receptor ADRM1 × 1 （Q16186） CHLORIDE ION × 4 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCHL5_HUMAN
Isoform	Q9Y5K5-3
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–328； UniProt 1–328

Proteasomal ubiquitin receptor ADRM1

Homo sapiens

UniProt Q16186

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5 × 1 （Q9Y5K5） Nb-cS1 × 1 CHLORIDE ION × 4 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ADRM1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 7–126； UniProt 269–388

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	9e7k
Deposition date deposition_date	2024-11-01
Last revision last_revision	2025-09-03
Structure title title	Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in the canonical ubiquitin binding site
Keywords keywords	Ubiquitin C-terminal Hydrolase, nanobody inhibitor, UCH37, RPN13, 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.

9e7k__assembly_1__model_1

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

Download this curve (.dat)

9e7k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9e7k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.10 Å
Rg (electron density)	25.18 Å
Total Rg	25.96 Å
Atom count	3686
Residues	485
Excluded volume	65329 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9e7k__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 (5)

Entity 1 Entity 1 polymer

Description description	Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5
Molecular weight formula_weight	37523.7 kDa
EC 编号 ec_number	3.4.19.12
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	3769

MTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK

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	Nb-cS1
Molecular weight formula_weight	14970.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGSSHHHHHHSSGLVPRGSHMQVQLQESGGGLVQAGGSLRLSCAASGYISRPRTMGWYRQAPGKEREFVAIISNGAITNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAGRNIWHAYWGQGTQVTVSS

Source Source

Source organism organism	Camelidae mixed library
NCBI taxonomy ID ncbi_taxonomy_id	1579311
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Proteasomal ubiquitin receptor ADRM1
Molecular weight formula_weight	12953.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPLGSMSILATMNVPAGPAGGQQVDLASVLTPEIMAPILANADVQERLLPYLPSGESLPQTADEIQNTLTSPQFQQALGMFSAALASGQLGPLMCQFGLPAEAVEAANKGDVEAFAKAMQNNAKPE

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 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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Unit-cell length a length_a	178.634 Å
Unit-cell length b length_b	190.732 Å
Unit-cell length c length_c	45.560 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.410 Å
Low-resolution limit resolution_low	37.310 Å
R factor r_factor	0.2363
R_work r_work	0.2346
R_free r_free	0.2705

Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in the canonical ubiquitin binding site

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

Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5

State in the Current Structure

Other States of the Same Protein in the Database

Proteasomal ubiquitin receptor ADRM1

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

9e7k__assembly_1__model_1

9e7k__assembly_1__model_1 | I(q)

9e7k__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in the canonical ubiquitin binding site

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

Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Proteasomal ubiquitin receptor ADRM1

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

9e7k__assembly_1__model_1

9e7k__assembly_1__model_1 | I(q)

9e7k__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)