5JJZ | pdb_00005jjz

Chromo domain of human Chromodomain Protein, Y-Like 2

PDB DOI: https://doi.org/10.2210/pdb5JJZ/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-04-25 Released: 2016-05-25
Deposition Author(s): DONG, A., DOMBROVSKI, L., LOPPNAU, P., TEMPEL, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., MIN, J., WU, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.260 (Depositor), 0.258 (DCC)
R-Value Work:
0.230 (Depositor), 0.233 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of CDYL2 domain of human CDYL2 protein

WU, H., DONG, A., ZENG, H., ELBAKKOURI, M., BARSYTE, D., VEDADI, M., TATLOCK, J., OWEN, D., BUNNAGE, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 11.55 kDa
Atom Count: 533
Modeled Residue Count: 63
Deposited Residue Count: 96
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromodomain Y-like protein 2	A	83	Homo sapiens	Mutation(s): 0 Gene Names: CDYL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N8U2 (Homo sapiens) Explore Q8N8U2 Go to UniProtKB: Q8N8U2
PHAROS: Q8N8U2 GTEx: ENSG00000166446
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N8U2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-LYS-LYS-ALA-ARG-MLY-SER-ALA-GLY-ALA-ALA-LYS-TYR	B	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10412 (Homo sapiens) Explore P10412 Go to UniProtKB: P10412
PHAROS: P10412 GTEx: ENSG00000168298
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10412
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	B	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.260 (Depositor), 0.258 (DCC)
R-Value Work: 0.230 (Depositor), 0.233 (DCC)
R-Value Observed: 0.232 (Depositor)

Diffraction Data:

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.962	α = 90
b = 57.962	β = 90
c = 98.824	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-05-25

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2016-05-25
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description