6V3N Gene Regulation date Nov 26, 2019
title Crystal Structure Of Cdyl2 In Complex With H3k27me3
authors S.Qin, W.Tempel, C.H.Arrowsmith, C.Bountra, A.M.Edwards, J.Min, St Genomics Consortium, Structural Genomics Consortium (Sgc)
compound source
Molecule: Chromodomain Y-Like Protein 2
Chain: A, B
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
Expression_system_taxid: 562

Molecule: Ace-Gln-Leu-Ala-Thr-Lys-Ala-Ala-Arg-M3l-Ser-Ala-P Thr-Tyr-Nh2;
Chain: C, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 43 2 2
R_factor 0.240 R_Free 0.258
length a length b length c angle alpha angle beta angle gamma
60.792 60.792 178.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand M3L, NH2, 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] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (6v3n.pdb1.gz) 27 Kb
  • Biological Unit Coordinates (6v3n.pdb2.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 6V3N
  • CSU: Contacts of Structural Units for 6V3N
  • Structure Factors (2066 Kb)
  • Retrieve 6V3N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6V3N from S2C, [Save to disk]
  • View 6V3N 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 6V3N
  • 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 6v3n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6v3n_C] [6v3n_A] [6v3n_D] [6v3n_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6V3N
  • Community annotation for 6V3N at PDBWiki (http://pdbwiki.org)

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