6C2F Dna Binding Protein Dna date Jan 08, 2018
title Mbd2 In Complex With Methylated Dna
authors K.Liu, C.Xu, W.Tempel, C.H.Arrowsmith, C.Bountra, A.M.Edwards, J.M Structural Genomics Consortium, Structural Genomics Consorti
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 2
Chain: A, D, G, J, M, P
Synonym: Demethylase,Dmtase,Methyl-Cpg-Binding Protein Mbd2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mbd2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-V2r-Prare2
Expression_system_plasmid: Pet28-Mhl

Molecule: 12-Mer Dna
Chain: B, E, H, K, N, Q
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic

Molecule: 12-Mer Dna
Chain: C, F, I, L, O, R
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic
symmetry Space Group: P 1
R_factor 0.212 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.510 40.600 202.380 90.07 93.11 119.75
method X-Ray Diffractionresolution 2.65 Å
ligand 5CM, UNX enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, J, M, D, P, G


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (265 Kb) [Save to disk]
  • Biological Unit Coordinates (6c2f.pdb1.gz) 45 Kb
  • Biological Unit Coordinates (6c2f.pdb2.gz) 44 Kb
  • Biological Unit Coordinates (6c2f.pdb3.gz) 45 Kb
  • Biological Unit Coordinates (6c2f.pdb4.gz) 43 Kb
  • Biological Unit Coordinates (6c2f.pdb5.gz) 43 Kb
  • Biological Unit Coordinates (6c2f.pdb6.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 6C2F
  • CSU: Contacts of Structural Units for 6C2F
  • Structure Factors (3279 Kb)
  • Retrieve 6C2F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6C2F from S2C, [Save to disk]
  • View 6C2F 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 6C2F
  • 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 6c2f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6c2f_L] [6c2f_R] [6c2f_O] [6c2f_H] [6c2f_J] [6c2f_M] [6c2f_D] [6c2f_A] [6c2f_P] [6c2f_N] [6c2f_Q] [6c2f_K] [6c2f_E] [6c2f_C] [6c2f_F] [6c2f_B] [6c2f_G] [6c2f_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6C2F
  • Community annotation for 6C2F at PDBWiki (http://pdbwiki.org)

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