1M54 Lyase date Jul 08, 2002
title Cystathionine-Beta Synthase: Reduced Vicinal Thiols
authors S.Taoka, B.W.Lepore, O.Kabil, S.Ojha, D.Ringe, R.Banerjee
compound source
Molecule: Cystathionine Beta-Synthase
Chain: A, B, C, D, E, F
Fragment: Residues 44-406
Synonym: Serine Sulfhydrase, Beta-Thionase
Ec: 4.2.1.22
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Blood
Gene: Cbs
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcbs-Deltan43deltac143
symmetry Space Group: P 1
R_factor 0.271 R_Free 0.365
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.740 85.626 97.082 102.01 101.53 112.60
method X-Ray Diffractionresolution 2.90 Å
ligand HEM, PLP enzyme Lyase E.C.4.2.1.22 BRENDA
related structures by homologous chain: 1JBQ
Primary referenceHuman cystathionine beta-synthase is a heme sensor protein. Evidence that the redox sensor is heme and not the vicinal cysteines in the CXXC motif seen in the crystal structure of the truncated enzyme., Taoka S, Lepore BW, Kabil O, Ojha S, Ringe D, Banerjee R, Biochemistry 2002 Aug 20;41(33):10454-61. PMID:12173932
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (339 Kb) [Save to disk]
  • Biological Unit Coordinates (1m54.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (1m54.pdb2.gz) 113 Kb
  • Biological Unit Coordinates (1m54.pdb3.gz) 114 Kb
  • LPC: Ligand-Protein Contacts for 1M54
  • CSU: Contacts of Structural Units for 1M54
  • Likely Quarternary Molecular Structure file(s) for 1M54
  • Structure Factors (714 Kb)
  • Retrieve 1M54 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M54 from S2C, [Save to disk]
  • Re-refined 1m54 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1M54 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 1M54
  • 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 1M54, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m54a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m54b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1m54c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1m54d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1m54e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1m54f_, region F [Jmol] [rasmolscript] [script source]
  • Fold representative 1m54 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: [1m54_C] [1m54_B] [1m54_A] [1m54_F] [1m54] [1m54_E] [1m54_D]
  • SWISS-PROT database: [P35520]
  • Domain organization of [CBS_HUMAN] by SWISSPFAM
  • Other resources with information on 1M54
  • Community annotation for 1M54 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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