3KD0 Oxidoreductase date Oct 22, 2009
title Human Thioredoxin C35s,C62s,C69s,C73s Mutant Showing Cadmium Bound To The Active Site
authors G.Hall, J.Emsley
compound source
Molecule: Thioredoxin
Chain: A
Synonym: Trx, Atl-Derived Factor, Adf, Surface-Associated S Protein, Sasp;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Htrx-1, Trdx, Trx, Trx1, Txn
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Tuner(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petblue-1
symmetry Space Group: P 61 2 2
R_factor 0.232 R_Free 0.279
length a length b length c angle alpha angle beta angle gamma
53.635 53.635 154.148 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.70 Å
ligand CD, CL enzyme

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk]
  • Biological Unit Coordinates (3kd0.pdb1.gz) 20 Kb
  • Biological Unit Coordinates (3kd0.pdb2.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 3KD0
  • CSU: Contacts of Structural Units for 3KD0
  • Structure Factors (219 Kb)
  • Retrieve 3KD0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KD0 from S2C, [Save to disk]
  • Re-refined 3kd0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KD0 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 3KD0
  • 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 3KD0, from MSDmotif at EBI
  • Fold representative 3kd0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kd0] [3kd0_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3KD0 with the sequences similar proteins can be viewed for 3KD0's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3KD0
  • Community annotation for 3KD0 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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