1VC8 Hydrolase date Mar 05, 2004
title Crystal Structure Of A T.Thermophilus Hb8 Ap6a Hydrolase Ndx Complex
authors T.Iwai, N.Nakagawa, S.Kuramitsu, R.Masui, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Ndx1
Chain: A, B
Synonym: Muttnudix Family Protein
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Ndx1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11b
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.413 54.775 111.673 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 5FA enzyme
related structures by homologous chain: 1VC9, 1VCD
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (1vc8.pdb1.gz) 24 Kb
  • Biological Unit Coordinates (1vc8.pdb2.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 1VC8
  • CSU: Contacts of Structural Units for 1VC8
  • Likely Quarternary Molecular Structure file(s) for 1VC8
  • Structure Factors (183 Kb)
  • Retrieve 1VC8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VC8 from S2C, [Save to disk]
  • Re-refined 1vc8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VC8 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 1VC8
  • 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
  • 3D motif for 1VC8, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vc8_B] [1vc8_A] [1vc8]
  • SWISS-PROT database: [Q75UV1]
  • Domain organization of [Q75UV1_THETH] by SWISSPFAM
    • Other resources with information on 1VC8
  • Community annotation for 1VC8 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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