3ODM Lyase date Aug 11, 2010
title Archaeal-Type Phosphoenolpyruvate Carboxylase
authors P.W.Dunten
compound source
Molecule: Phosphoenolpyruvate Carboxylase
Chain: A, B, C, D, E, F, G, H
Synonym: Pepcase, Pepc
Engineered: Yes
Organism_scientific: Clostridium Perfringens
Organism_taxid: 1502
Gene: Cpe1094, Ppca
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)(Pril)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pjlk15-19b
symmetry Space Group: P 21 21 21
R_factor 0.178 R_Free 0.223
length a length b length c angle alpha angle beta angle gamma
121.420 161.580 279.980 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.95 Å
ligand AUC, MLI enzyme Lyase E.C. BRENDA
F, A, E, B, H, C, D, G

Primary referenceStructure of an archaeal-type phosphoenolpyruvate carboxylase sensitive to inhibition by aspartate., Dharmarajan L, Kraszewski JL, Mukhopadhyay B, Dunten PW, Proteins. 2011 Feb 3. doi: 10.1002/prot.23006. PMID:21491491
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1420 Kb) [Save to disk]
  • Biological Unit Coordinates (3odm.pdb1.gz) 704 Kb
  • Biological Unit Coordinates (3odm.pdb2.gz) 706 Kb
  • Biological Unit Coordinates (3odm.pdb3.gz) 355 Kb
  • Biological Unit Coordinates (3odm.pdb4.gz) 357 Kb
  • Biological Unit Coordinates (3odm.pdb5.gz) 357 Kb
  • Biological Unit Coordinates (3odm.pdb6.gz) 357 Kb
  • LPC: Ligand-Protein Contacts for 3ODM
  • CSU: Contacts of Structural Units for 3ODM
  • Structure Factors (2584 Kb)
  • Retrieve 3ODM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ODM from S2C, [Save to disk]
  • Re-refined 3odm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ODM 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 3ODM
  • 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 3ODM, from MSDmotif at EBI
  • Fold representative 3odm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3odm] [3odm_H] [3odm_D] [3odm_C] [3odm_F] [3odm_B] [3odm_E] [3odm_A] [3odm_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3ODM
  • Community annotation for 3ODM 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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