SAXSdb — 5yt6

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

Ubiquitin

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	Tax1-binding protein 1 × 1 （Q86VP1） ZINC ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Tax1-binding protein 1 × 1 （Q86VP1） ZINC ION × 1 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Tax1-binding protein 1 × 1 （Q86VP1） ZINC ION × 1 SULFATE ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Tax1-binding protein 1 × 1 （Q86VP1） ZINC ION × 1 GLYCEROL × 1 1,2-ETHANEDIOL × 1 water × 2	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–78； UniProt 77–152 Author chain C； PDBConstruct 3–78； UniProt 77–152 Author chain E； PDBConstruct 3–78； UniProt 77–152 Author chain G； PDBConstruct 3–78； UniProt 77–152

Tax1-binding protein 1

Homo sapiens

UniProt Q86VP1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin × 1 （P0CG47） ZINC ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin × 1 （P0CG47） ZINC ION × 1 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin × 1 （P0CG47） ZINC ION × 1 SULFATE ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin × 1 （P0CG47） ZINC ION × 1 GLYCEROL × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TAXB1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–35； UniProt 754–787 Author chain D； PDBConstruct 2–35； UniProt 754–787 Author chain F； PDBConstruct 2–35； UniProt 754–787 Author chain H； PDBConstruct 2–35； UniProt 754–787

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	5yt6
Deposition date deposition_date	2017-11-17
Structure title title	Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin
Keywords keywords	TAX1BP1, ubiquitin, complex, autophagy receptor, 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.

5yt6__assembly_1__model_1

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

Download this curve (.dat)

5yt6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5yt6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.47 Å
Rg (electron density)	14.08 Å
Total Rg	15.17 Å
Atom count	898
Residues	110
Excluded volume	15980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5yt6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5yt6__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5yt6__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5yt6__assembly_4__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 (7)

Entity 1 Entity 1 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8721.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,A,C,G
Atom count atom_count	3900

GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Tax1-binding protein 1
Molecular weight formula_weight	4257.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,B,D,H

SWKVCPMCSEQFPPDYDQQVFERHVQTHFDQNVLN

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-Gold(DE3)pLysS AG' ;

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	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	357

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5yt6a1
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	d5yt6a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5yt6c1
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	d5yt6c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5yt6e1
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	d5yt6e2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5yt6g1
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	d5yt6g2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	48.709 Å
Unit-cell length b length_b	72.938 Å
Unit-cell length c length_c	119.879 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	16

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

Resolution resolution	1.501 Å
Low-resolution limit resolution_low	30.894 Å
R factor r_factor	0.1950
R_work r_work	0.1934
R_free r_free	0.2252

Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin

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

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Tax1-binding protein 1

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

5yt6__assembly_1__model_1

5yt6__assembly_1__model_1 | I(q)

5yt6__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)

Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin

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

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tax1-binding protein 1

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

5yt6__assembly_1__model_1

5yt6__assembly_1__model_1 | I(q)

5yt6__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)