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6v8w

CDYL2 chromodomain in complex with a synthetic peptide

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chromodomain Y-like protein 2

Homo sapiens

UniProt Q8N8U2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 3 Consistent with protein count
10 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
11 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
12 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 Consistent with protein count
13 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
14 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 2 Consistent with protein count
15 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
16 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 Consistent with protein count
17 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
18 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 Consistent with protein count
19 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 Consistent with protein count
20 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
21 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 Consistent with protein count
22 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 Consistent with protein count
23 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 Consistent with protein count
24 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
25 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
26 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 2 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 4 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count
9 Protein heterocomplex Heteromer Protein 2 IVA-PHE-ALA-PHE-5T3-SER-NH2 × 1 UNKNOWN LIGAND × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2mj8

1 assemblies

Homodimer
4hae

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5jjz 5jjz 6v2d 6v2d 6v2d 6v2d 6v2d 6v2d 6v2h 6v2h 6v2h 6v2h

48 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CDYL2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–62； UniProt 2–62 Author chain B； PDBConstruct 2–62； UniProt 2–62 Author chain C； PDBConstruct 2–62； UniProt 2–62 Author chain D； PDBConstruct 2–62； UniProt 2–62 Author chain E； PDBConstruct 2–62； UniProt 2–62 Author chain F； PDBConstruct 2–62； UniProt 2–62 Author chain G； PDBConstruct 2–62； UniProt 2–62 Author chain H； PDBConstruct 2–62； UniProt 2–62 Author chain I； PDBConstruct 2–62； UniProt 2–62 Author chain J； PDBConstruct 2–62； UniProt 2–62 Author chain K； PDBConstruct 2–62； UniProt 2–62 Author chain L； PDBConstruct 2–62； UniProt 2–62 Author chain M； PDBConstruct 2–62； UniProt 2–62 Author chain N； PDBConstruct 2–62； UniProt 2–62 Author chain O； PDBConstruct 2–62； UniProt 2–62 Author chain P； PDBConstruct 2–62； UniProt 2–62 Author chain Q； PDBConstruct 2–62； UniProt 2–62 Author chain R； PDBConstruct 2–62； UniProt 2–62 Author chain S； PDBConstruct 2–62； UniProt 2–62 Author chain T； PDBConstruct 2–62； UniProt 2–62 Author chain U； PDBConstruct 2–62； UniProt 2–62 Author chain V； PDBConstruct 2–62； UniProt 2–62 Author chain W； PDBConstruct 2–62； UniProt 2–62 Author chain X； PDBConstruct 2–62； UniProt 2–62 Author chain Y； PDBConstruct 2–62； UniProt 2–62 Author chain Z； PDBConstruct 2–62； UniProt 2–62

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_id6v8w
Deposition date deposition_date2019-12-12
Structure title titleCDYL2 chromodomain in complex with a synthetic peptide
Keywords keywordschromodomain, Structural Genomics, Structural Genomics Consortium, SGC, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-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.

6v8w__assembly_2__model_1

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

Download this curve (.dat)

6v8w__assembly_2__model_1 | I(q)

10-2 10-1 105 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6v8w__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）13.26 Å
Rg (electron density)12.22 Å
Total Rg13.52 Å
Atom count472
Residues54
Excluded volume8383 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6v8w__assembly_1__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.
2 1 6v8w__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6v8w__assembly_3__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.
4 1 6v8w__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 6v8w__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 6v8w__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.
7 1 6v8w__assembly_7__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.
8 1 6v8w__assembly_8__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.
9 1 6v8w__assembly_9__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.
10 1 6v8w__assembly_10__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.
11 1 6v8w__assembly_11__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.
12 1 6v8w__assembly_12__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
13 1 6v8w__assembly_13__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.
14 1 6v8w__assembly_14__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.
15 1 6v8w__assembly_15__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.
16 1 6v8w__assembly_16__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
17 1 6v8w__assembly_17__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.
18 1 6v8w__assembly_18__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
19 1 6v8w__assembly_19__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.
20 1 6v8w__assembly_20__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.
21 1 6v8w__assembly_21__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
22 1 6v8w__assembly_22__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
23 1 6v8w__assembly_23__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
24 1 6v8w__assembly_24__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.
25 1 6v8w__assembly_25__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.
26 1 6v8w__assembly_26__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 (3)

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7. Citations (1)