SAXSdb — 6at0

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

Heterochromatin protein 1

Drosophila melanogaster

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 17–76	Fragment：Chromo 1 domain, residues 17-76 Mutation：K38M Non-standard monomer：Yes (specific site not provided by mmCIF)	trimethyl lysine histone H3 tail peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.8；277 K；0.1M MES, 3.0M (NH4)2SO4	Resolution 1.28 Å R-free 0.260

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6AT0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KNA Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9. Deposited 2001-12-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–76（60 aa） Fragment：Residues 23-76	Mutation：K38M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；283 K；Ammonium Sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283.0K	Resolution 2.10 Å R-free 0.259
1KNE Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9 Deposited 2001-12-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–76（60 aa） Fragment：Residues 17-76	Mutation：K38M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；283 K；Ammonium Sulfate, MES, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 2.40 Å R-free 0.267
1Q3L Chromodomain Of HP1 Complexed With Histone H3 Tail Containing monomethyllysine 9. Deposited 2003-07-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–76（60 aa） Fragment：sequence database residues 17-76	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；283 K；Ammonium Sulfate, MES, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 1.64 Å R-free 0.241
3P7J Drosophila HP1a chromo shadow domain Deposited 2010-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 131–206（76 aa） Fragment：UNP residues 131-206 Chain B 131–206（76 aa） Fragment：UNP residues 131-206	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；12% PEG400, 0.1 M HEPES. Cryoprotected in 12% PEG400, 0.1 M HEPES, 33% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.246
3P7J Drosophila HP1a chromo shadow domain Deposited 2010-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 131–206（76 aa） Fragment：UNP residues 131-206 Chain B 131–206（76 aa） Fragment：UNP residues 131-206	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；12% PEG400, 0.1 M HEPES. Cryoprotected in 12% PEG400, 0.1 M HEPES, 33% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.246
6ASZ Chromodomain HP1 with Y24F mutation bound to histone H3 peptide containing trimethyl lysine Deposited 2017-08-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–76（60 aa） Fragment：Chromo 1 domain, residues 17-76	Mutation：Y24F , K38M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；277 K；0.1 M MES, 3.4 M (NH4)2SO4	Resolution 1.52 Å R-free 0.274
6MHA dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine Deposited 2018-09-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 22–74（53 aa）	Mutation：Y24W, K38M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；3.2 M Ammonium sulfate, 0.1 M MES	Resolution 1.50 Å R-free 0.219

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HP1_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–69； UniProt 17–76

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	6at0
Deposition date deposition_date	2017-08-27
Structure title title	Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone H3 peptide containing trimethyl lysine
Keywords keywords	histone reader, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	12.42 Å
Radius of gyration Rg (electron density) rg_electron	10.93 Å
Forward intensity I(0) i0	1272670.00
Molecular weight molecular_weight	7255.0 kDa
Excluded volume excluded_volume	8970 Å³
Envelope volume envelope_volume	9940 Å³
Hydration-shell volume shell_volume	8014 Å³
Envelope diameter envelope_diameter	35.1 Å
Shell Rg shell_rg	16.27 Å
Envelope Rg envelope_rg	11.30 Å
Shape Rg shape_rg	10.89 Å
Total Rg total_rg	12.44 Å
Total atoms total_atoms	511
Residues n_residues	57
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	38.0 Å
Rg (real space) rg_real	12.33 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	1.2730e+06
I(0) uncertainty (real space) i0_real_error	1.1620e+04
Rg (reciprocal space) rg_reciprocal	12.33 Å
I(0) (reciprocal space) i0_reciprocal	1273000.0000
Solution quality estimate total_estimate	0.9021
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.9 Å
Skewness Skewness skewness	0.109
Kurtosis Kurtosis kurtosis	-0.384
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	230700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.958

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Heterochromatin protein 1
Molecular weight formula_weight	8615.5 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	579

MKKHHHHHHAEEEEEEFAVEKIIDRRVRKGMVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKD

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	trimethyl lysine histone H3 tail peptide
Molecular weight formula_weight	733.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

QTARKS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6at0A00
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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8. Citations (1)

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Unit-cell length a length_a	34.417 Å
Unit-cell length b length_b	76.857 Å
Unit-cell length c length_c	76.479 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	1.285 Å
Low-resolution limit resolution_low	11.224 Å
R factor r_factor	0.2418
R_work r_work	0.2410
R_free r_free	0.2597

fit	/app/data/saxs_computation/at/6at0/6at0.fit
pddf	/app/data/pr_computation/at/6at0/6at0.pr.out
profile	/app/data/saxs_computation/at/6at0/6at0.dat

Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone H3 peptide containing trimethyl lysine

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)