6V2D Gene Regulation date Nov 22, 2019
title Crystal Structure Of Chromodomain Of Cdyl2 In Complex With I Unc3866
authors Y.Liu, W.Tempel, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, St 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: Unc3866
Chain: J, L, B, D, F, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.212 R_Free 0.268
length a length b length c angle alpha angle beta angle gamma
45.979 83.835 115.288 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 5R0, 5R5, ELY, 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] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (6v2d.pdb1.gz) 14 Kb
  • Biological Unit Coordinates (6v2d.pdb2.gz) 15 Kb
  • Biological Unit Coordinates (6v2d.pdb3.gz) 14 Kb
  • Biological Unit Coordinates (6v2d.pdb4.gz) 15 Kb
  • Biological Unit Coordinates (6v2d.pdb5.gz) 14 Kb
  • Biological Unit Coordinates (6v2d.pdb6.gz) 13 Kb
  • LPC: Ligand-Protein Contacts for 6V2D
  • CSU: Contacts of Structural Units for 6V2D
  • Structure Factors (3493 Kb)
  • Retrieve 6V2D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6V2D from S2C, [Save to disk]
  • View 6V2D 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 6V2D
  • 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 6v2d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6v2d_E] [6v2d_I] [6v2d_C] [6v2d_A] [6v2d_G] [6v2d_J] [6v2d_H] [6v2d_D] [6v2d_K] [6v2d_F] [6v2d_L] [6v2d_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6V2D
  • Community annotation for 6V2D at PDBWiki (http://pdbwiki.org)

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