3U1K Transferase date Sep 30, 2011
title Crystal Structure Of Human Pnpase
authors C.L.Lin, H.S.Yuan
compound source
Molecule: Polyribonucleotide Nucleotidyltransferase 1, Mito
Chain: A, C, B, D
Fragment: Unp Residues 46-669
Synonym: 3'-5' Rna Exonuclease Old35, Pnpase Old-35, Polynu Phosphorylase 1, Pnpase 1, Polynucleotide Phosphorylase-Lik
Ec: 2.7.7.8
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pnpt1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: H 3
R_factor 0.180 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
289.753 289.753 92.785 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.13 Å
ligand CIT enzyme Transferase E.C.2.7.7.8 BRENDA
Primary referenceCrystal structure of human polynucleotide phosphorylase: insights into its domain function in RNA binding and degradation., Lin CL, Wang YT, Yang WZ, Hsiao YY, Yuan HS, Nucleic Acids Res. 2011 Dec 30. PMID:22210891
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (413 Kb) [Save to disk]
  • Biological Unit Coordinates (3u1k.pdb1.gz) 308 Kb
  • Biological Unit Coordinates (3u1k.pdb2.gz) 305 Kb
  • LPC: Ligand-Protein Contacts for 3U1K
  • CSU: Contacts of Structural Units for 3U1K
  • Structure Factors (2400 Kb)
  • Retrieve 3U1K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3U1K from S2C, [Save to disk]
  • Re-refined 3u1k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3U1K 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 3U1K
  • 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 3U1K, from MSDmotif at EBI
  • Fold representative 3u1k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3u1k_A] [3u1k_B] [3u1k_C] [3u1k_D] [3u1k]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3U1K: [KH ] by SMART
  • Other resources with information on 3U1K
  • Community annotation for 3U1K at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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