4YOC Transferase Hydrolase date Mar 11, 2015
title Crystal Structure Of Human Dnmt1 And Usp7hausp Complex
authors J.Cheng, H.Yang, J.Fang, R.Gong, P.Wang, Z.Li, Y.Xu
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 1
Chain: A
Fragment: Unp Residues 600-1600
Synonym: Dnmt1,Cxxc-Type Zinc Finger Protein 9,Dna Methyltr Hsai,M.Hsai,Mcmt;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt1, Aim, Cxxc9, Dnmt
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 7
Chain: C
Fragment: Unp Residues 560-1102
Synonym: Deubiquitinating Enzyme 7,Herpesvirus-Associated U Specific Protease,Ubiquitin Thioesterase 7,Ubiquitin-Specif Processing Protease 7;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Usp7, Hausp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.258
length a length b length c angle alpha angle beta angle gamma
110.231 111.619 163.868 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.92 Å
ligand ZN enzyme Transferase E.C. BRENDA

Primary referenceMolecular mechanism for USP7-mediated DNMT1 stabilization by acetylation., Cheng J, Yang H, Fang J, Ma L, Gong R, Wang P, Li Z, Xu Y, Nat Commun. 2015 May 11;6:7023. doi: 10.1038/ncomms8023. PMID:25960197
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (239 Kb) [Save to disk]
  • Biological Unit Coordinates (4yoc.pdb1.gz) 233 Kb
  • LPC: Ligand-Protein Contacts for 4YOC
  • CSU: Contacts of Structural Units for 4YOC
  • Structure Factors (1178 Kb)
  • Retrieve 4YOC in mmCIF format [Save to disk]
  • Re-refined 4yoc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YOC 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 4YOC
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4YOC, from MSDmotif at EBI
  • Fold representative 4yoc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yoc_A] [4yoc] [4yoc_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4YOC: [BAH ] by SMART
  • Other resources with information on 4YOC
  • Community annotation for 4YOC at PDBWiki (http://pdbwiki.org)

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