SAXSdb — 3dm1

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

Chromobox protein homolog 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	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 1 （Q96KQ7） water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 1 （Q96KQ7） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 1 （Q96KQ7） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 1 （Q96KQ7） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 8	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 4 （Q96KQ7） water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBX3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–58； UniProt 29–86 Author chain C； PDBConstruct 1–58； UniProt 29–86 Author chain E； PDBConstruct 1–58； UniProt 29–86 Author chain G； PDBConstruct 1–58； UniProt 29–86

Histone-lysine N-methyltransferase, H3 lysine-9 specific 3

OrganismNot specified

UniProt Q96KQ7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Chromobox protein homolog 3 × 1 （Q13185） water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Chromobox protein homolog 3 × 1 （Q13185） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Chromobox protein homolog 3 × 1 （Q13185） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Chromobox protein homolog 3 × 1 （Q13185） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 8	Chromobox protein homolog 3 × 4 （Q13185） water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EHMT2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–12； UniProt 179–190 Author chain D； PDBConstruct 1–12； UniProt 179–190 Author chain F； PDBConstruct 1–12； UniProt 179–190 Author chain H； PDBConstruct 1–12； UniProt 179–190

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	3dm1
Deposition date deposition_date	2008-06-30
Structure title title	Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide
Keywords keywords	;Chromobox homolog 3, Structural Genomics, Structural Genomics Consortium, SGC, Chromatin regulator, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription regulation ;; TRANSCRIPTION
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.

3dm1__assembly_1__model_1

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

Download this curve (.dat)

3dm1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dm1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	12.50 Å
Rg (electron density)	11.16 Å
Total Rg	12.62 Å
Atom count	494
Residues	59
Excluded volume	8791 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dm1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dm1__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3dm1__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3dm1__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3dm1__assembly_5__model_1`	octameric （8）	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	Chromobox protein homolog 3
Molecular weight formula_weight	6812.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	2109

EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQKAGKEK

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3
Molecular weight formula_weight	1486.9 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

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

KVHRARKTMSKP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3dm1A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3dm1C00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3dm1E00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3dm1G00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	83.671 Å
Unit-cell length b length_b	83.671 Å
Unit-cell length c length_c	110.288 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	24

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	39.100 Å
R factor r_factor	0.2219
R_work r_work	0.2195
R_free r_free	0.2672

Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide

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

Chromobox protein homolog 3

State in the Current Structure

Other States of the Same Protein in the Database

Histone-lysine N-methyltransferase, H3 lysine-9 specific 3

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

3dm1__assembly_1__model_1

3dm1__assembly_1__model_1 | I(q)

3dm1__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)

Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide

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

Chromobox protein homolog 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

Histone-lysine N-methyltransferase, H3 lysine-9 specific 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dm1__assembly_1__model_1

3dm1__assembly_1__model_1 | I(q)

3dm1__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)