SAXSdb — 4wlr

▼

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

Ubiquitin carboxyl-terminal hydrolase isozyme L5

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Proteasomal ubiquitin receptor ADRM1 × 1 （Q16186） Polyubiquitin-B × 1 （P0CG47） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCHL5_MOUSE
Isoform	—
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	Ubiquitin carboxyl-terminal hydrolase isozyme L5 × 1 （Q9WUP7） Polyubiquitin-B × 1 （P0CG47） 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–102； UniProt 285–386

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 isozyme L5 × 1 （Q9WUP7） Proteasomal ubiquitin receptor ADRM1 × 1 （Q16186） 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	3
Chains and sequence ranges	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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4wlr
Deposition date deposition_date	2014-10-07
Structure title title	Crystal Structure of mUCH37-hRPN13 CTD-hUb complex
Keywords keywords	UCH37 RPN13 Proteasome INO80 DUB, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4wlr__assembly_1__model_1

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

Download this curve (.dat)

4wlr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4wlr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.63 Å
Rg (electron density)	24.62 Å
Total Rg	25.46 Å
Atom count	3719
Residues	471
Excluded volume	66480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4wlr__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase isozyme L5
Molecular weight formula_weight	37533.7 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	3920

MSSNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPESFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLETIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTPAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWITAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGSTVLSAIQSEVARNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Proteasomal ubiquitin receptor ADRM1
Molecular weight formula_weight	10719.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVDLASVLTPEIMAPILANADVQERLLPYLPSGESLPQTADEIQNTLTSPQFQQALGMFSAALASGQLGPLMCQFGLPAEAVEAANKGDVEAFAKAMQNNAK

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 polymer

Description description	Polyubiquitin-B
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	201

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4wlrc_
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 (3 domains)

Domain ID domain_id	4wlrA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	532 — Ubiquitin C-terminal Hydrolase UCH-l3
Homologous superfamily homologous superfamily	10 — Peptidase C12, ubiquitin carboxyl-terminal hydrolase

Domain ID domain_id	4wlrA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	860 —

Domain ID domain_id	4wlrB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2020 — uronate isomerase, domain 2, chain A
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	60.120 Å
Unit-cell length b length_b	99.610 Å
Unit-cell length c length_c	99.909 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.997 Å
Low-resolution limit resolution_low	38.422 Å
R factor r_factor	0.1828
R_work r_work	0.1806
R_free r_free	0.2273

Crystal Structure of mUCH37-hRPN13 CTD-hUb complex

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

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

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

4wlr__assembly_1__model_1

4wlr__assembly_1__model_1 | I(q)

4wlr__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of mUCH37-hRPN13 CTD-hUb complex

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

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

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

4wlr__assembly_1__model_1

4wlr__assembly_1__model_1 | I(q)

4wlr__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)