SAXSdb — 3evx

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

Ufm1-conjugating enzyme 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	THIOCYANATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	THIOCYANATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	THIOCYANATE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	THIOCYANATE ION × 1 water × 1	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 1–167 Author chain B； PDBConstruct 1–167； UniProt 1–167 Author chain C； PDBConstruct 1–167； UniProt 1–167 Author chain D； 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	3evx
Deposition date deposition_date	2008-10-13
Structure title title	Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41
Keywords keywords	;alpha-beta protein, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Polymorphism, Ubl conjugation pathway, 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.

3evx__assembly_1__model_1

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

Download this curve (.dat)

3evx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3evx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.13 Å
Rg (electron density)	15.86 Å
Total Rg	17.03 Å
Atom count	1305
Residues	156
Excluded volume	23402 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3evx__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3evx__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3evx__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3evx__assembly_4__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	Ufm1-conjugating enzyme 1
Molecular weight formula_weight	20698.2 kDa
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	5389

MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCNQLEHHHHHH

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	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3evxa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.4 — UFC1-like

Domain ID domain_id	d3evxb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.4 — UFC1-like

Domain ID domain_id	d3evxc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.4 — UFC1-like

Domain ID domain_id	d3evxd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.4 — UFC1-like

CATH v4.4 (4 domains)

Domain ID domain_id	3evxA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	3evxB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	3evxC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	3evxD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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Unit-cell length a length_a	41.368 Å
Unit-cell length b length_b	64.537 Å
Unit-cell length c length_c	66.422 Å
Unit-cell angle α angle_alpha	90.06 °
Unit-cell angle β angle_beta	89.95 °
Unit-cell angle γ angle_gamma	105.18 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.540 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2790

Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41

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

Ufm1-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

3evx__assembly_1__model_1

3evx__assembly_1__model_1 | I(q)

3evx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41

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

Ufm1-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

3evx__assembly_1__model_1

3evx__assembly_1__model_1 | I(q)

3evx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)