SAXSdb — 7n27

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

Isoform 2 of Chromodomain Y-like protein

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	inhibitor UNC6261 × 1 SODIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	inhibitor UNC6261 × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	inhibitor UNC6261 × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	inhibitor UNC6261 × 1 SODIUM ION × 1 UNKNOWN ATOM OR ION × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	inhibitor UNC6261 × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	inhibitor UNC6261 × 1 UNKNOWN ATOM OR ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDYL_HUMAN
Isoform	Q9Y232-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–57； UniProt 4–59 Author chain B； PDBConstruct 2–57； UniProt 4–59 Author chain C； PDBConstruct 2–57； UniProt 4–59 Author chain D； PDBConstruct 2–57； UniProt 4–59 Author chain E； PDBConstruct 2–57； UniProt 4–59 Author chain F； PDBConstruct 2–57； UniProt 4–59

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	7n27
Deposition date deposition_date	2021-05-28
Structure title title	Crystal Structure of chromodomain of CDYL in complex with inhibitor UNC6261
Keywords keywords	;Chromodomain Y-like protein, transcription regulation, spermatogenesis, Structural Genomics, Structural Genomics Consortium, SGC, TRANSCRIPTION ;; 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.

7n27__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7n27__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7n27__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	12.84 Å
Rg (electron density)	11.30 Å
Total Rg	12.68 Å
Atom count	554
Residues	60
Excluded volume	9581 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7n27__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7n27__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7n27__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7n27__assembly_4__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
5	1	`7n27__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`7n27__assembly_6__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Isoform 2 of Chromodomain Y-like protein
Molecular weight formula_weight	7125.8 kDa
EC 编号 ec_number	4.2.1.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	3279

GEELYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHDFNRRH

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	inhibitor UNC6261
Molecular weight formula_weight	920.0 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

XFAFXA

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	69

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Unit-cell length a length_a	62.971 Å
Unit-cell length b length_b	76.386 Å
Unit-cell length c length_c	80.628 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	48.640 Å
R factor r_factor	0.2270
R_work r_work	0.2250
R_free r_free	0.2620

Crystal Structure of chromodomain of CDYL in complex with inhibitor UNC6261

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

Isoform 2 of Chromodomain Y-like protein

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

7n27__assembly_2__model_1

7n27__assembly_2__model_1 | I(q)

7n27__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal Structure of chromodomain of CDYL in complex with inhibitor UNC6261

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

Isoform 2 of Chromodomain Y-like protein

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

7n27__assembly_2__model_1

7n27__assembly_2__model_1 | I(q)

7n27__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)