SAXSdb — 3fdt

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

Chromobox protein homolog 5

Homo sapiens

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 18–75	Not recorded	H3K9(me)3 peptide × 1 （Q3BDD9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；35% PEG 400, 0.2M Na Cl, 0.1M Tris (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.257

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 3FDT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3I3C Crystal Structural of CBX5 Chromo Shadow Domain Deposited 2009-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–173（64 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；20% PEG3350, 0.2M di-Na Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.48 Å R-free 0.303
3I3C Crystal Structural of CBX5 Chromo Shadow Domain Deposited 2009-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 110–173（64 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；20% PEG3350, 0.2M di-Na Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.48 Å R-free 0.303
3I3C Crystal Structural of CBX5 Chromo Shadow Domain Deposited 2009-06-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 110–173（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；20% PEG3350, 0.2M di-Na Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.48 Å R-free 0.303
3I3C Crystal Structural of CBX5 Chromo Shadow Domain Deposited 2009-06-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 110–173（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；20% PEG3350, 0.2M di-Na Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.48 Å R-free 0.303
8UXQ Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Deposited 2023-11-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric	Chain A 2–191（190 aa） Chain C 2–191（190 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.30 Å
9CDW Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide Deposited 2024-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 111–174（64 aa） Chain C 111–174（64 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris pH 5.8, 0.2 M MgCl2, 20% PEG3350, 30 mM glycyl-glycyl-glycine	Resolution 2.40 Å R-free 0.252
9CDW Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide Deposited 2024-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 111–174（64 aa） Chain D 111–174（64 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris pH 5.8, 0.2 M MgCl2, 20% PEG3350, 30 mM glycyl-glycyl-glycine	Resolution 2.40 Å R-free 0.252
9CEA Crystal structure of HP1alpha chromoshadow domain Deposited 2024-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 113–175（63 aa） Chain B 113–175（63 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7, 0.2 M sodium chloride and 20% w/v PEG6000	Resolution 2.15 Å R-free 0.277
9CEA Crystal structure of HP1alpha chromoshadow domain Deposited 2024-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 113–175（63 aa） Chain D 113–175（63 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7, 0.2 M sodium chloride and 20% w/v PEG6000	Resolution 2.15 Å R-free 0.277
9CMT The crystal structure of HP1alpha CSD-Agno complex Deposited 2024-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 112–176（65 aa） Chain B 112–176（65 aa） Chain D 112–176（65 aa） Chain E 112–176（65 aa）	Mutation：C133S, T145S Mutation：C133S, T145S Mutation：C133S, T145S Mutation：C133S, T145S	F6Z 3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-5-CARBOXYLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1 uL protein solution (about 10 mg/ml) and 1 uL reservoir solution containing 0.01 M NiCl2, 0.1 M Tris-HCl, pH 8.5, and 20% PEG2000MME (v/v)	Resolution 3.17 Å R-free 0.286

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBX5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–59； UniProt 18–75

H3K9(me)3 peptide

OrganismNot specified

UniProt Q3BDD9

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 T； UniProt 2–16	Non-standard monomer：Yes (specific site not provided by mmCIF)	Chromobox protein homolog 5 × 1 （P45973）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；35% PEG 400, 0.2M Na Cl, 0.1M Tris (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.257

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 3FDT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L3R NMR structure of UHRF1 Tandem Tudor Domains in a complex with Histone H3 peptide Deposited 2010-09-21	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–12（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR sample composition 0.6 mM [U-100% 15N] protein, 0.6 mM [U-100% 13C] protein, 3 mM protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q3BDD9_9INSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain T； PDBConstruct 1–15； UniProt 2–16

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3fdt
Deposition date deposition_date	2008-11-26
Structure title title	Crystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3 peptide
Keywords keywords	;chromobox homolog5, CBX5, H3K9(me)3 peptide, Structural Genomics, Structural Genomics Consortium, SGC, Centromere, Nucleus, Phosphoprotein, Chromosomal protein, DNA-binding, Nucleosome core, PROTEIN BINDING ;; PROTEIN BINDING
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	12.54 Å
Radius of gyration Rg (electron density) rg_electron	11.20 Å
Forward intensity I(0) i0	1087690.00
Molecular weight molecular_weight	7016.0 kDa
Excluded volume excluded_volume	8839 Å³
Envelope volume envelope_volume	9883 Å³
Hydration-shell volume shell_volume	7860 Å³
Envelope diameter envelope_diameter	43.0 Å
Shell Rg shell_rg	16.36 Å
Envelope Rg envelope_rg	11.88 Å
Shape Rg shape_rg	11.15 Å
Total Rg total_rg	12.72 Å
Total atoms total_atoms	495
Residues n_residues	60
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	44.6 Å
Rg (real space) rg_real	12.50 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	1.0880e+06
I(0) uncertainty (real space) i0_real_error	1.2460e+04
Rg (reciprocal space) rg_reciprocal	12.50 Å
I(0) (reciprocal space) i0_reciprocal	1088000.0000
Solution quality estimate total_estimate	0.8493
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.2 Å
Skewness Skewness skewness	0.260
Kurtosis Kurtosis kurtosis	-0.142
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	213700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.697; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.976

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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	Chromobox protein homolog 5
Molecular weight formula_weight	7205.3 kDa
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	529

GEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMKKYKKMKE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	H3K9(me)3 peptide
Molecular weight formula_weight	1607.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

ARTKQTARKSTGGKA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3fdtA00
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	73.123 Å
Unit-cell length b length_b	73.123 Å
Unit-cell length c length_c	28.413 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	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	51.710 Å
R factor r_factor	0.1993
R_work r_work	0.1966
R_free r_free	0.2574

fit	/app/data/saxs_computation/fd/3fdt/3fdt.fit
pddf	/app/data/pr_computation/fd/3fdt/3fdt.pr.out
profile	/app/data/saxs_computation/fd/3fdt/3fdt.dat

Crystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3 peptide

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

Chromobox protein homolog 5

State in the Current Structure

Other States of the Same Protein in the Database

H3K9(me)3 peptide

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)