1M65 Structural Genomics, Unknown Function date Jul 12, 2002
title Ycdx Protein
authors A.Teplyakov, G.Obmolova, P.P.Khil, R.D.Camerini-Otero, G.L.Gilli Structure 2 Function Project (S2f)
compound source
Molecule: Hypothetical Protein Ycdx
Chain: A
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pdest14
symmetry Space Group: P 3 2 1
R_factor 0.177 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.230 77.230 79.990 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.57 Å
ligand NA, SO4, ZN enzyme
related structures by homologous chain: 1PB0
Gene
Ontology
ChainFunctionProcessComponent
A
  • phosphatase activity


    • Primary referenceCrystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site., Teplyakov A, Obmolova G, Khil PP, Howard AJ, Camerini-Otero RD, Gilliland GL, Proteins 2003 May 1;51(2):315-8. PMID:12661000
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (1m65.pdb1.gz) 126 Kb
  • LPC: Ligand-Protein Contacts for 1M65
  • CSU: Contacts of Structural Units for 1M65
  • Likely Quarternary Molecular Structure file(s) for 1M65
  • Structure Factors (697 Kb)
  • Retrieve 1M65 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M65 from S2C, [Save to disk]
  • Re-refined 1m65 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1M65 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 1M65
  • 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 1M65, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m65a_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1m65_A] [1m65]
  • SWISS-PROT database: [P75914]
  • Domain organization of [YCDX_ECOLI] by SWISSPFAM
  • Domain found in 1M65: [POLIIIAc ] by SMART
    • Other resources with information on 1M65
  • Community annotation for 1M65 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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