SAXSdb — 3hym

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

Anaphase-promoting complex subunit CDC26

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	Cell division cycle protein 16 homolog × 1 （Q13042） water × 2	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 12	Cell division cycle protein 16 homolog × 6 （Q13042） water × 12	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cell division cycle protein 16 homolog × 1 （Q13042） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Cell division cycle protein 16 homolog × 1 （Q13042） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Cell division cycle protein 16 homolog × 1 （Q13042） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Cell division cycle protein 16 homolog × 1 （Q13042） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Cell division cycle protein 16 homolog × 1 （Q13042） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 4	Cell division cycle protein 16 homolog × 2 （Q13042） water × 4	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 4	Cell division cycle protein 16 homolog × 2 （Q13042） water × 4	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 4	Cell division cycle protein 16 homolog × 2 （Q13042） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDC26_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–29； UniProt 1–29 Author chain C； PDBConstruct 1–29； UniProt 1–29 Author chain E； PDBConstruct 1–29； UniProt 1–29 Author chain G； PDBConstruct 1–29； UniProt 1–29 Author chain I； PDBConstruct 1–29； UniProt 1–29 Author chain K； PDBConstruct 1–29； UniProt 1–29

Cell division cycle protein 16 homolog

Homo sapiens

UniProt Q13042

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Anaphase-promoting complex subunit CDC26 × 1 （Q8NHZ8） water × 2	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 12	Anaphase-promoting complex subunit CDC26 × 6 （Q8NHZ8） water × 12	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Anaphase-promoting complex subunit CDC26 × 1 （Q8NHZ8） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Anaphase-promoting complex subunit CDC26 × 1 （Q8NHZ8） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Anaphase-promoting complex subunit CDC26 × 1 （Q8NHZ8） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Anaphase-promoting complex subunit CDC26 × 1 （Q8NHZ8） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Anaphase-promoting complex subunit CDC26 × 1 （Q8NHZ8） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 4	Anaphase-promoting complex subunit CDC26 × 2 （Q8NHZ8） water × 4	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 4	Anaphase-promoting complex subunit CDC26 × 2 （Q8NHZ8） water × 4	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 4	Anaphase-promoting complex subunit CDC26 × 2 （Q8NHZ8） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDC16_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–330； UniProt 212–539 Author chain D； PDBConstruct 3–330； UniProt 212–539 Author chain F； PDBConstruct 3–330； UniProt 212–539 Author chain H； PDBConstruct 3–330； UniProt 212–539 Author chain J； PDBConstruct 3–330； UniProt 212–539 Author chain L； PDBConstruct 3–330； UniProt 212–539

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	3hym
Deposition date deposition_date	2009-06-22
Structure title title	Insights into Anaphase Promoting Complex TPR subdomain assembly from a CDC26-APC6 structure
Keywords keywords	;APC, Anaphase Promoting Complex, Cell Cycle, Mitosis, Cyclosome, TPR, Ubiquitin, Ubiquitin Ligase, E3, twinning, Alternative splicing, Cell division, Phosphoprotein, TPR repeat, Ubl conjugation pathway, Coiled coil, Nucleus, LIGASE ;; CELL CYCLE, 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.

3hym__assembly_7__model_1

Assembly 7 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3hym__assembly_7__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hym__assembly_7__model_1 | P(r) · Pending

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

Rg（Guinier）	29.35 Å
Rg (electron density)	28.77 Å
Total Rg	29.67 Å
Atom count	5122
Residues	632
Excluded volume	91312 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hym__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3hym__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3hym__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3hym__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3hym__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3hym__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3hym__assembly_7__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3hym__assembly_8__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3hym__assembly_9__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3hym__assembly_10__model_1`	dodecameric （12）	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	Anaphase-promoting complex subunit CDC26
Molecular weight formula_weight	3713.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	15517

MLRRKPTRLELKLDDIEEFENIRKDLETR

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	Cell division cycle protein 16 homolog
Molecular weight formula_weight	37806.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

GSYNKPSETVIPESVDGLQENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTALGLRRDDTFSVTMLGHCIEMYIGDSEAYIGADIK

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3hymB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3hymD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3hymF00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3hymH00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3hymJ00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3hymL00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

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Unit-cell length a length_a	301.897 Å
Unit-cell length b length_b	301.897 Å
Unit-cell length c length_c	80.168 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	49.400 Å
R factor r_factor	0.1894
R_work r_work	0.1879
R_free r_free	0.2197

Insights into Anaphase Promoting Complex TPR subdomain assembly from a CDC26-APC6 structure

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

Anaphase-promoting complex subunit CDC26

State in the Current Structure

Other States of the Same Protein in the Database

Cell division cycle protein 16 homolog

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

3hym__assembly_7__model_1

3hym__assembly_7__model_1 | I(q)

3hym__assembly_7__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Insights into Anaphase Promoting Complex TPR subdomain assembly from a CDC26-APC6 structure

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

Anaphase-promoting complex subunit CDC26

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cell division cycle protein 16 homolog

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

3hym__assembly_7__model_1

3hym__assembly_7__model_1 | I(q)

3hym__assembly_7__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)