SAXSdb — 4gba

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

DCN1-like protein 3

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	NEDD8-conjugating enzyme UBE2F × 1 （Q969M7） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	NEDD8-conjugating enzyme UBE2F × 1 （Q969M7） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCNL3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–221； UniProt 86–304 Author chain B； PDBConstruct 3–221； UniProt 86–304

NEDD8-conjugating enzyme UBE2F

OrganismNot specified

UniProt Q969M7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DCN1-like protein 3 × 1 （Q8IWE4） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DCN1-like protein 3 × 1 （Q8IWE4） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBE2F_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain F； PDBConstruct 1–25； UniProt 1–25 Author chain G； PDBConstruct 1–25； UniProt 1–25

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	4gba
Deposition date deposition_date	2012-07-26
Structure title title	DCNL complex with N-terminally acetylated NEDD8 E2 peptide
Keywords keywords	E3 ligase, ligase-peptide complex; ligase/peptide
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.

4gba__assembly_1__model_1

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

Download this curve (.dat)

4gba__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4gba__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.10 Å
Rg (electron density)	18.80 Å
Total Rg	19.64 Å
Atom count	1684
Residues	204
Excluded volume	29673 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4gba__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4gba__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 (3)

Entity 1 Entity 1 polymer

Description description	DCN1-like protein 3
Molecular weight formula_weight	25671.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3559

GSSSLQRLEELFRRYKDEREDAILEEGMERFCNDLCVDPTEFRVLLLAWKFQAATMCKFTRKEFFDGCKAISADSIDGICARFPSLLTEAKQEDKFKDLYRFTFQFGLDSEEGQRSLHREIAIALWKLVFTQNNPPVLDQWLNFLTENPSGIKGISRDTWNMFLNFTQVIGPDLSNYSEDEAWPSLFDTFVEWEMERRKREGEGRGALSSGPEGLCPEEQT

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	NEDD8-conjugating enzyme UBE2F
Molecular weight formula_weight	2654.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

MLTLASKLKRDDGLKGSRTAATASD

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	132

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4gbaA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4gbaA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	200 — Cullin, PONY binding domain

Domain ID domain_id	4gbaB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4gbaB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	200 — Cullin, PONY binding domain

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Unit-cell length a length_a	83.465 Å
Unit-cell length b length_b	44.578 Å
Unit-cell length c length_c	101.216 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	29.085 Å
R factor r_factor	0.1956
R_work r_work	0.1939
R_free r_free	0.2273

DCNL complex with N-terminally acetylated NEDD8 E2 peptide

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

DCN1-like protein 3

State in the Current Structure

Other States of the Same Protein in the Database

NEDD8-conjugating enzyme UBE2F

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

4gba__assembly_1__model_1

4gba__assembly_1__model_1 | I(q)

4gba__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

DCNL complex with N-terminally acetylated NEDD8 E2 peptide

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

DCN1-like protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NEDD8-conjugating enzyme UBE2F

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

4gba__assembly_1__model_1

4gba__assembly_1__model_1 | I(q)

4gba__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)