1Z4K Hydrolase date Mar 16, 2005
title Structure Of The D41n Variant Of The Human Mitochondrial Deoxyribonucleotidase In Complex With Thymidine 3'- Monophosphate
authors K.Wallden, B.Ruzzenente, A.Rinaldo-Matthis, V.Bianchi, P.Nordlund
compound source
Molecule: 5'(3')-Deoxyribonucleotidase
Chain: A
Synonym: Mitochondrial Deoxyribonucleotidase, 5',3'- Nucleotidase, Mitochondrial, Deoxy-5'-Nucleotidase 2, Dnt- 2;
Ec: 3.1.3.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plyss
symmetry Space Group: P 43 21 2
R_factor 0.167 R_Free 0.183
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.180 73.180 105.920 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand MG, T3P enzyme Hydrolase E.C.3.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase., Wallden K, Ruzzenente B, Rinaldo-Matthis A, Bianchi V, Nordlund P, Structure (Camb) 2005 Jul;13(7):1081-8. PMID:16004879
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (1z4k.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 1Z4K
  • CSU: Contacts of Structural Units for 1Z4K
  • Likely Quarternary Molecular Structure file(s) for 1Z4K
  • Structure Factors (242 Kb)
  • Retrieve 1Z4K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Z4K from S2C, [Save to disk]
  • Re-refined 1z4k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Z4K 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 1Z4K
  • 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 1Z4K, from MSDmotif at EBI
  • Fold representative 1z4k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1z4k] [1z4k_A]
  • SWISS-PROT database: [Q9NPB1]
  • Domain organization of [NT5M_HUMAN] by SWISSPFAM
  • Other resources with information on 1Z4K
  • Community annotation for 1Z4K 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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