3CLZ Ligase date Mar 20, 2008
title The Set And Ring Associated (Sra) Domain Of Uhrf1 Bound To Methylated Dna
authors J.R.Walker, G.V.Avvakumov, S.Xue, A.Dong, Y.Li, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe- Paganon, Structural Genomics Consortium (Sgc)
compound source
Molecule: E3 Ubiquitin-Protein Ligase Uhrf1
Chain: A, B, C, D
Fragment: Sra Domain (Unp Residues 414-617)
Synonym: Ubiquitin-Like Phd And Ring Finger Domain- Containing Protein 1, Ubiquitin-Like-Containing Phd And Ring Finger Domains Protein 1, Inverted Ccaat Box-Binding Protein Of 90 Kda, Transcription Factor Icbp90, Nuclear Zinc Finger Protein Np95, Nuclear Protein 95, Hunp95, Ring Finger Protein 106;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Uhrf1, Icbp90, Np95, Rnf106
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Ch

Molecule: 5'-D(Dgpdgpdgpdcpdcp(5cm) Pdgpdcpdapdgpdgpdg)-3';
Chain: E, G, I, K
Engineered: Yes

Synthetic: Yes

Molecule: 5'- D(Dcpdcpdcpdtpdgpdcpdgpdgpdgpdcpdcpdc)-3';
Chain: F, H, J, L
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.189 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.198 111.359 97.403 90.00 90.53 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 5CM enzyme Ligase E.C.6.3.2 BRENDA
Primary referenceStructural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1., Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner C, Arrowsmith CH, Dhe-Paganon S, Nature. 2008 Oct 9;455(7214):822-5. Epub 2008 Sep 3. PMID:18772889
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (379 Kb) [Save to disk]
  • Biological Unit Coordinates (3clz.pdb1.gz) 93 Kb
  • Biological Unit Coordinates (3clz.pdb2.gz) 93 Kb
  • Biological Unit Coordinates (3clz.pdb3.gz) 92 Kb
  • Biological Unit Coordinates (3clz.pdb4.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 3CLZ
  • CSU: Contacts of Structural Units for 3CLZ
  • Likely Quarternary Molecular Structure file(s) for 3CLZ
  • Structure Factors (1307 Kb)
  • Retrieve 3CLZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CLZ from S2C, [Save to disk]
  • Re-refined 3clz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CLZ 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 3CLZ
  • 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 3CLZ, from MSDmotif at EBI
  • Fold representative 3clz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3clz_L] [3clz] [3clz_B] [3clz_H] [3clz_A] [3clz_K] [3clz_C] [3clz_J] [3clz_G] [3clz_I] [3clz_E] [3clz_F] [3clz_D]
  • SWISS-PROT database: [Q96T88]
  • Domain organization of [UHRF1_HUMAN] by SWISSPFAM
  • Domain found in 3CLZ: [SRA ] by SMART
  • Other resources with information on 3CLZ
  • Community annotation for 3CLZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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