SAXSdb — 3tdi

▼

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

Defective in cullin neddylation protein 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	NEDD8-conjugating enzyme UBC12 × 1 （P52491） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	NEDD8-conjugating enzyme UBC12 × 1 （P52491） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	NEDD8-conjugating enzyme UBC12 × 2 （P52491） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCN1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–202； UniProt 70–269 Author chain B； PDBConstruct 3–202； UniProt 70–269

NEDD8-conjugating enzyme UBC12

Saccharomyces cerevisiae

UniProt P52491

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Defective in cullin neddylation protein 1 × 2 （Q12395） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Defective in cullin neddylation protein 1 × 2 （Q12395） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Defective in cullin neddylation protein 1 × 2 （Q12395） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC12_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–25； UniProt 2–24 Author chain D； PDBConstruct 3–25； UniProt 2–24

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3tdi
Deposition date deposition_date	2011-08-11
Structure title title	yeast Cul1WHB-Dcn1P acetylated Ubc12N complex
Keywords keywords	E2:E3, Ligase-protein binding complex; Ligase/protein binding
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3tdi__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3tdi__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3tdi__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.64 Å
Rg (electron density)	24.24 Å
Total Rg	25.11 Å
Atom count	3639
Residues	427
Excluded volume	65440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3tdi__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3tdi__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3tdi__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Defective in cullin neddylation protein 1
Molecular weight formula_weight	24353.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	3788

GSVYPKELTQVFEHYINNNLFDIDSLVKFIEELGYNLEDLATLCLAHLLGYKKLEEPLKREDFLSTWFMQGCSTISDMQECIKTLDVKLHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFLRDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYECLQDQQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	NEDD8-conjugating enzyme UBC12
Molecular weight formula_weight	2902.4 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

XMLKLRQLQKKKQKENENSSSIQPN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3tdiA01
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	3tdiB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

▶

Unit-cell length a length_a	72.906 Å
Unit-cell length b length_b	98.421 Å
Unit-cell length c length_c	143.923 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	37.000 Å
R factor r_factor	0.2058
R_work r_work	0.2027
R_free r_free	0.2661

yeast Cul1WHB-Dcn1P acetylated Ubc12N complex

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

Defective in cullin neddylation protein 1

State in the Current Structure

Other States of the Same Protein in the Database

NEDD8-conjugating enzyme UBC12

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

3tdi__assembly_3__model_1

3tdi__assembly_3__model_1 | I(q)

3tdi__assembly_3__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

yeast Cul1WHB-Dcn1P acetylated Ubc12N complex

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

Defective in cullin neddylation 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

NEDD8-conjugating enzyme UBC12

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

3tdi__assembly_3__model_1

3tdi__assembly_3__model_1 | I(q)

3tdi__assembly_3__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)