SAXSdb — 4wlp

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

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 2	Nuclear factor related to kappa-B-binding protein × 1 （Q6P4R8）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Nuclear factor related to kappa-B-binding protein × 2 （Q6P4R8）	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 1–317； UniProt 5–321

Nuclear factor related to kappa-B-binding protein

Homo sapiens

UniProt Q6P4R8

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 isozyme L5 × 1 （Q9Y5K5）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Ubiquitin carboxyl-terminal hydrolase isozyme L5 × 2 （Q9Y5K5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NFRKB_HUMAN
Isoform	Q6P4R8-2
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–114； UniProt 53–166

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	4wlp
Deposition date deposition_date	2014-10-07
Structure title title	Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating Complex
Keywords keywords	UCH37 NFRKB Proteasome INO80 DUB, PROTEIN BINDING; 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.

4wlp__assembly_1__model_1

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

Download this curve (.dat)

4wlp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4wlp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.48 Å
Rg (electron density)	24.48 Å
Total Rg	25.39 Å
Atom count	3352
Residues	410
Excluded volume	59641 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4wlp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4wlp__assembly_2__model_1`	tetrameric （4）	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 (2)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase isozyme L5
Molecular weight formula_weight	36303.3 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	3352

AGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNA

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	Nuclear factor related to kappa-B-binding protein
Molecular weight formula_weight	13651.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EDLLEDPEIFFDVVSLSTWQEVLSDSQREHLQQFLPQFPEDSAEQQNELILALFSGENFRFGNPLHIAQKLFRDGHFNPEVVKYRQLCFKSQYKRYLNSQQQYFHRLLKQILAS

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

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4wlpA01
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

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Unit-cell length a length_a	95.488 Å
Unit-cell length b length_b	95.488 Å
Unit-cell length c length_c	131.964 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	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	3.102 Å
Low-resolution limit resolution_low	38.680 Å
R factor r_factor	0.1999
R_work r_work	0.1932
R_free r_free	0.2680

Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating 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

Nuclear factor related to kappa-B-binding protein

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

4wlp__assembly_1__model_1

4wlp__assembly_1__model_1 | I(q)

4wlp__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating 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

Nuclear factor related to kappa-B-binding 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4wlp__assembly_1__model_1

4wlp__assembly_1__model_1 | I(q)

4wlp__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)