6UHG

crytal structure of CDY1 chromodomain bound to H3K9me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.602 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

crytal structure of CDY1 chromodomain bound to H3K9me3

Qin, S.Tempel, W.Walker, J.R.Arrowsmith, C.H.Bountra, C.Edwards, A.M.Min, J.Structural Genomics Consortium

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Testis-specific chromodomain protein Y 1
AAA
63Homo sapiensMutation(s): 0 
Gene Names: CDY1, CDY1B (CDY1A)
EC: 2.3.1.48
Find proteins for Q9Y6F8 (Homo sapiens)
Go to Gene View: CDY1 CDY1B
Go to UniProtKB:  Q9Y6F8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
QQQ
15Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
AAA, QQQ
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
QQQ
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 42.450α = 90.00
b = 42.450β = 90.00
c = 37.200γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling
REFMACrefinement
ARP/wARPmodel building
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release