1CMX Hydrolase date May 12, 1999
title Structural Basis For The Specificity Of Ubiquitin C- Terminal Hydrolases
authors S.C.Johnston, S.M.Riddle, R.E.Cohen, C.P.Hill
compound source
Molecule: Protein (Ubiquitin Yuh1-Ubal)
Chain: A, C
Fragment: All
Ec: 3.1.2.15
Engineered: Yes
Other_details: Ubiquitin C-Terminus Modified To An Aldehyde;
Synthetic: Yes
Other_details: The Protein Was Chemically Synthesized. The Sequence Of This Protein Is Naturally Found In The Cytoplasm Of Plasmid P-1a2trpyuh1-1 Of Saccharomyces Cerevisiae (Baker'S Yeast). The Expression System Was Escherichia Coli, Strain Mm294, Plasmid P-1a2trpyuh1-1.;

Molecule: Protein (Ubiquitin Yuh1-Ubal)
Chain: B, D
Fragment: All
Ec: 3.1.2.15
Engineered: Yes
Other_details: Ubiquitin C-Terminus Modified To An Aldehyde

Synthetic: Yes
Other_details: The Protein Was Chemically Synthesized. The Sequence Of This Protein Is Naturally Found In The Cytoplasm Of Plasmid P-1a2trpyuh1-1 Of Saccharomyces Cerevisiae (Baker'S Yeast). The Expression System Was Escherichia Coli, Strain Mm294, Plasmid P-1a2trpyuh1-1.
symmetry Space Group: H 3
R_factor 0.248 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
199.300 199.300 36.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.25 Å
ligand GLZ enzyme Hydrolase E.C.3.1.2.15 BRENDA
related structures by homologous chain: 1AAR, 1SIF
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • thiol-dependent ubiquitin-sp...


  • Primary referenceStructural basis for the specificity of ubiquitin C-terminal hydrolases., Johnston SC, Riddle SM, Cohen RE, Hill CP, EMBO J 1999 Jul 15;18(14):3877-87. PMID:10406793
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (1cmx.pdb1.gz) 86 Kb
  • LPC: Ligand-Protein Contacts for 1CMX
  • CSU: Contacts of Structural Units for 1CMX
  • Likely Quarternary Molecular Structure file(s) for 1CMX
  • Structure Factors (192 Kb)
  • Retrieve 1CMX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1CMX from S2C, [Save to disk]
  • Re-refined 1cmx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1CMX 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 1CMX
  • 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 1CMX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1cmxa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1cmxb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1cmxc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1cmxd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1cmx from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1cmx_C] [1cmx] [1cmx_B] [1cmx_A] [1cmx_D]
  • SWISS-PROT database: [P62988] [P35127]
  • Domain organization of [UBIQ_HUMAN] [UBL1_YEAST] by SWISSPFAM
  • Domain found in 1CMX: [UBQ ] by SMART
  • Other resources with information on 1CMX
  • Community annotation for 1CMX 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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