4L57 Hydrolase date Jun 10, 2013
title High Resolutin Structure Of Human Cytosolic 5'(3')- Deoxyribonucleotidase
authors P.Pachl, J.Brynda, P.Rezacova
compound source
Molecule: 5'(3')-Deoxyribonucleotidase, Cytosolic Type
Chain: A, B
Fragment: Unp Residues 1-195
Synonym: Cytosolic 5',3'-Pyrimidine Nucleotidase, Deoxy-5'- Nucleotidase 1, Dnt-1;
Ec: 3.1.3.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnt1, Nt5c, Umph2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet 22
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.128 46.493 61.409 68.16 81.47 75.28
method X-Ray Diffractionresolution 1.08 Å
ligand GOL, MG, NA, PO4 enzyme Hydrolase E.C.3.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors., Pachl P, Fabry M, Rosenberg I, Simak O, Rezacova P, Brynda J, Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):461-70. doi:, 10.1107/S1399004713030502. Epub 2014 Jan 29. PMID:24531480
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (155 Kb) [Save to disk]
  • Biological Unit Coordinates (4l57.pdb1.gz) 150 Kb
  • LPC: Ligand-Protein Contacts for 4L57
  • CSU: Contacts of Structural Units for 4L57
  • Structure Factors (1181 Kb)
  • Retrieve 4L57 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4L57 from S2C, [Save to disk]
  • Re-refined 4l57 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4L57 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 4L57
  • 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
  • 3D motif for 4L57, from MSDmotif at EBI
  • Fold representative 4l57 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4l57_B] [4l57] [4l57_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4L57
  • Community annotation for 4L57 at PDBWiki (http://pdbwiki.org)

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