6V2H Gene Regulation date Nov 22, 2019
title Crystal Structure Of Cdyl2 In Complex With H3tk27me3
authors C.Dong, W.Tempel, J.R.Walker, C.Bountra, C.H.Arrowsmith, A.M.Edwa J.Min, Structural Genomics Consortium (Sgc)
compound source
Molecule: Chromodomain Y-Like Protein 2
Chain: A, C, E, G, I, K
Fragment: Chromodomain
Synonym: Cdy-Like 2, Cdyl2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdyl2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: -V2r-Prare2
Expression_system_plasmid: Pet28-Mhl

Molecule: H3tk27me3
Chain: B, D, F, H, J, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Other_details: Synthetic Peptide
symmetry Space Group: H 3
R_factor 0.217 R_Free 0.237
length a length b length c angle alpha angle beta angle gamma
210.750 210.750 67.200 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand ACE, M3L, NI, UNX enzyme
Primary referenceStructural Basis for the Binding Selectivity of Human CDY Chromodomains., Dong C, Liu Y, Lyu TJ, Beldar S, Lamb KN, Tempel W, Li Y, Li Z, James LI, Qin S, Wang Y, Min J, Cell Chem Biol. 2020 May 26. pii: S2451-9456(20)30153-7. doi:, 10.1016/j.chembiol.2020.05.007. PMID:32470319
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (155 Kb) [Save to disk]
  • Biological Unit Coordinates (6v2h.pdb1.gz) 26 Kb
  • Biological Unit Coordinates (6v2h.pdb2.gz) 27 Kb
  • Biological Unit Coordinates (6v2h.pdb3.gz) 27 Kb
  • Biological Unit Coordinates (6v2h.pdb4.gz) 27 Kb
  • Biological Unit Coordinates (6v2h.pdb5.gz) 27 Kb
  • Biological Unit Coordinates (6v2h.pdb6.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 6V2H
  • CSU: Contacts of Structural Units for 6V2H
  • Structure Factors (3844 Kb)
  • Retrieve 6V2H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6V2H from S2C, [Save to disk]
  • View 6V2H in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6V2H
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6v2h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6v2h_L] [6v2h_I] [6v2h_K] [6v2h_E] [6v2h_C] [6v2h_A] [6v2h_G] [6v2h_F] [6v2h_B] [6v2h_J] [6v2h_D] [6v2h_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6V2H
  • Community annotation for 6V2H at PDBWiki (http://pdbwiki.org)

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