SAXSdb — 1kne

▼

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

HETEROCHROMATIN PROTEIN 1

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Trimethylated Histone H3 × 1 （P02299） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HP1_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 17–76

Trimethylated Histone H3

OrganismNot specified

UniProt P02299

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	HETEROCHROMATIN PROTEIN 1 × 1 （P05205） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H3_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–16； UniProt 1–16

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	1kne
Deposition date deposition_date	2001-12-18
Structure title title	Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9
Keywords keywords	chromo, HP1, histone, trimethyllysine, methyllysine, H3, chromatin, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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.

1kne__assembly_1__model_1

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

Download this curve (.dat)

1kne__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kne__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	12.32 Å
Rg (electron density)	10.85 Å
Total Rg	12.36 Å
Atom count	500
Residues	57
Excluded volume	8815 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kne__assembly_1__model_1`	dimeric （2）	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	HETEROCHROMATIN PROTEIN 1
Molecular weight formula_weight	8586.5 kDa
Mutation mutation	K38M
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	571

MKKHHHHHHAEEEEEEYAVEKIIDRRVRKGMVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKD

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Trimethylated Histone H3
Molecular weight formula_weight	1771.1 kDa
Mutation mutation	P16Y
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ARTKQTARKSTGGKAY

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1knea_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.2 — Chromo domain

CATH v4.4 (1 domains)

Domain ID domain_id	1kneA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

▶

Unit-cell length a length_a	33.745 Å
Unit-cell length b length_b	76.943 Å
Unit-cell length c length_c	75.947 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	28.620 Å
R factor r_factor	—
R_work r_work	0.2460
R_free r_free	0.2670

Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9

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

HETEROCHROMATIN PROTEIN 1

State in the Current Structure

Other States of the Same Protein in the Database

Trimethylated Histone H3

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

1kne__assembly_1__model_1

1kne__assembly_1__model_1 | I(q)

1kne__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9

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

HETEROCHROMATIN 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

Trimethylated Histone H3

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

1kne__assembly_1__model_1

1kne__assembly_1__model_1 | I(q)

1kne__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)