SAXSdb — 8c0d

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

E3 UFM1-protein ligase 1

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	DDRGK domain-containing protein 1 × 1 （Q96HY6） Ubiquitin-fold modifier-conjugating enzyme 1 × 1 （Q9Y3C8） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	DDRGK domain-containing protein 1 × 1 （Q96HY6） Ubiquitin-fold modifier-conjugating enzyme 1 × 1 （Q9Y3C8） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UFL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 16–194； UniProt 1–179 Author chain D； PDBConstruct 16–194； UniProt 1–179

DDRGK domain-containing protein 1

Homo sapiens

UniProt Q96HY6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	E3 UFM1-protein ligase 1 × 1 （O94874） Ubiquitin-fold modifier-conjugating enzyme 1 × 1 （Q9Y3C8） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	E3 UFM1-protein ligase 1 × 1 （O94874） Ubiquitin-fold modifier-conjugating enzyme 1 × 1 （Q9Y3C8） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDRGK_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–110； UniProt 205–314 Author chain E； PDBConstruct 1–110； UniProt 205–314

Ubiquitin-fold modifier-conjugating enzyme 1

Homo sapiens

UniProt Q9Y3C8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	E3 UFM1-protein ligase 1 × 1 （O94874） DDRGK domain-containing protein 1 × 1 （Q96HY6） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	E3 UFM1-protein ligase 1 × 1 （O94874） DDRGK domain-containing protein 1 × 1 （Q96HY6） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UFC1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–167； UniProt 1–167 Author chain F； PDBConstruct 1–167； UniProt 1–167

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	8c0d
Deposition date deposition_date	2022-12-16
Structure title title	UFL1/DDRGK1 bound to UFC1
Keywords keywords	UFM1, E3 ligase, ubiquitin, UFBP1, 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.

8c0d__assembly_1__model_1

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

Download this curve (.dat)

8c0d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8c0d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.36 Å
Rg (electron density)	29.86 Å
Total Rg	30.25 Å
Atom count	6499
Residues	431
Excluded volume	58172 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8c0d__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8c0d__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	E3 UFM1-protein ligase 1
Molecular weight formula_weight	22350.3 kDa
EC 编号 ec_number	2.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	12907

MGHHHHHHENLYFQGMADAWEEIRRLAADFQRAQFAEATQRLSERNCIEIVNKLIAQKQLEVVHTLDGKEYITPAQISKEMRDELHVRGGRVNIVDLQQVINVDLIHIENRIGDIIKSEKHVQLVLGQLIDENYLDRLAEEVNDKLQESGQVTISELCKTYDLPGNFLTQALTQRLGRIISGHIDLDNRGVIFT

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	DDRGK domain-containing protein 1
Molecular weight formula_weight	12177.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

ETMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGLRTQDTINRIQDLLAEGTITGVIDDRGKFIYITPEELAAVANFIRQRGRVSIAELAQASNSLIAWGRESPAQAPA

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	Ubiquitin-fold modifier-conjugating enzyme 1
Molecular weight formula_weight	19569.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKIKLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCNQG

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	7

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Unit-cell length a length_a	79.210 Å
Unit-cell length b length_b	124.565 Å
Unit-cell length c length_c	131.292 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.564 Å
Low-resolution limit resolution_low	65.732 Å
R factor r_factor	—
R_work r_work	0.2320
R_free r_free	0.2858

UFL1/DDRGK1 bound to UFC1

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

E3 UFM1-protein ligase 1

State in the Current Structure

Other States of the Same Protein in the Database

DDRGK domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-fold modifier-conjugating enzyme 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

8c0d__assembly_1__model_1

8c0d__assembly_1__model_1 | I(q)

8c0d__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

7. Citations (1)

UFL1/DDRGK1 bound to UFC1

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

E3 UFM1-protein ligase 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

DDRGK domain-containing 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

Ubiquitin-fold modifier-conjugating enzyme 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

8c0d__assembly_1__model_1

8c0d__assembly_1__model_1 | I(q)

8c0d__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

7. Citations (1)