SAXSdb — 13se

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

E3 ubiquitin-protein ligase MYLIP

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MYLIP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–78； UniProt 369–445 Author chain B； PDBConstruct 2–78； UniProt 369–445 Author chain C； PDBConstruct 2–78； UniProt 369–445 Author chain D； PDBConstruct 2–78； UniProt 369–445

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	13se
Deposition date deposition_date	2025-10-10
Structure title title	PanDDA analysis group deposition -- IDOL RING domain in complex with Z1587220559
Keywords keywords	Diamond I04-1 fragment screening, PanDDA, XChemExplorer, E3, ubiquitin, Zinc finger, RING, ligase; LIGASE
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.

13se__assembly_1__model_1

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

Download this curve (.dat)

13se__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

13se__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.60 Å
Rg (electron density)	16.77 Å
Total Rg	17.56 Å
Atom count	1080
Residues	138
Excluded volume	19189 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`13se__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`13se__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase MYLIP
Molecular weight formula_weight	8820.4 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2729

SQQTRVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTSLLNLTVI

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol
Molecular weight formula_weight	239.3 kDa
Source method src_method	syn
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	297

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Unit-cell length a length_a	44.700 Å
Unit-cell length b length_b	48.020 Å
Unit-cell length c length_c	70.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.440 Å
Low-resolution limit resolution_low	20.930 Å
R factor r_factor	0.1739
R_work r_work	0.1727
R_free r_free	0.1978

PanDDA analysis group deposition -- IDOL RING domain in complex with Z1587220559

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

E3 ubiquitin-protein ligase MYLIP

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

13se__assembly_1__model_1

13se__assembly_1__model_1 | I(q)

13se__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

PanDDA analysis group deposition -- IDOL RING domain in complex with Z1587220559

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

E3 ubiquitin-protein ligase MYLIP

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

13se__assembly_1__model_1

13se__assembly_1__model_1 | I(q)

13se__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)