3U53 Hydrolase date Oct 10, 2011
title Crystal Structure Of Human Ap4a Hydrolase
authors H.H.Ge, M.K.Teng
compound source
Molecule: Bis(5'-Nucleosyl)-Tetraphosphatase [Asymmetrical]
Chain: A, B, C, D
Synonym: Asymmetrical Diadenosine Tetraphosphate Hydrolase, Hydrolase, Ap4aase, Nudix Hydrolase;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nudt2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 43
R_factor 0.213 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
72.485 72.485 133.491 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.71 Å
ligand GOL, SO4 enzyme Hydrolase E.C. BRENDA
A, D, C, B

Primary referenceCrystal structure of wild-type and mutant human Ap4A hydrolase., Ge H, Chen X, Yang W, Niu L, Teng M, Biochem Biophys Res Commun. 2013 Mar 1;432(1):16-21. doi:, 10.1016/j.bbrc.2013.01.095. Epub 2013 Feb 4. PMID:23384440
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (208 Kb) [Save to disk]
  • Biological Unit Coordinates (3u53.pdb1.gz) 51 Kb
  • Biological Unit Coordinates (3u53.pdb2.gz) 52 Kb
  • Biological Unit Coordinates (3u53.pdb3.gz) 51 Kb
  • Biological Unit Coordinates (3u53.pdb4.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 3U53
  • CSU: Contacts of Structural Units for 3U53
  • Structure Factors (243 Kb)
  • Retrieve 3U53 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3U53 from S2C, [Save to disk]
  • Re-refined 3u53 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3U53 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 3U53
  • 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 3U53, from MSDmotif at EBI
  • Fold representative 3u53 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3u53_B] [3u53_D] [3u53_A] [3u53] [3u53_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3U53
  • Community annotation for 3U53 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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