1JPM Isomerase date Aug 02, 2001
title L-Ala-Dl-Glu Epimerase
authors A.M.Gulick, D.M.Z.Schmidt, J.A.Gerlt, I.Rayment
compound source
Molecule: L-Ala-Dl-Glu Epimerase
Chain: A, B, C, D
Fragment: L-Ala-Dl-Glu Epimerase
Engineered: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: Ykfb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet
Expression_system_plasmid: Pet
symmetry Space Group: I 4
R_factor 0.197 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
157.630 157.630 168.320 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand GOL, MG enzyme
related structures by homologous chain: 1TKK
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceEvolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis., Gulick AM, Schmidt DM, Gerlt JA, Rayment I, Biochemistry 2001 Dec 25;40(51):15716-24. PMID:11747448
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (227 Kb) [Save to disk]
  • Biological Unit Coordinates (1jpm.pdb1.gz) 222 Kb
  • LPC: Ligand-Protein Contacts for 1JPM
  • CSU: Contacts of Structural Units for 1JPM
  • Likely Quarternary Molecular Structure file(s) for 1JPM
  • Structure Factors (848 Kb)
  • Retrieve 1JPM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JPM from S2C, [Save to disk]
  • Re-refined 1jpm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JPM 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 1JPM
  • 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 1JPM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jpma2, region A:1-125 [Jmol] [rasmolscript] [script source]
        - Domain d1jpma1, region A:126-359 [Jmol] [rasmolscript] [script source]
        - Domain d1jpmb2, region B:1-125 [Jmol] [rasmolscript] [script source]
        - Domain d1jpmb1, region B:126-359 [Jmol] [rasmolscript] [script source]
        - Domain d1jpmc2, region C:1-125 [Jmol] [rasmolscript] [script source]
        - Domain d1jpmc1, region C:126-358 [Jmol] [rasmolscript] [script source]
        - Domain d1jpmd2, region D:1-125 [Jmol] [rasmolscript] [script source]
        - Domain d1jpmd1, region D:126-358 [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: [1jpm] [1jpm_A] [1jpm_B] [1jpm_C] [1jpm_D]
  • SWISS-PROT database: [O34508]
  • Domain organization of [AEEP_BACSU] by SWISSPFAM
  • Domain found in 1JPM: [MR_MLE ] by SMART
  • Other resources with information on 1JPM
  • Community annotation for 1JPM 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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