2NMP Lyase date Oct 23, 2006
title Crystal Structure Of Human Cystathionine Gamma Lyase
authors T.Karlberg, J.Uppenberg, C.Arrowsmith, H.Berglund, R.D.Busam, R.C A.Edwards, U.B.Ericsson, S.Flodin, A.Flores, S.Graslund, B.M.Hal M.Hammarstrom, M.Hogbom, I.Johansson, T.Kotenyova, A.Magnusdott M.Moche, M.E.Nilsson, P.Nordlund, T.Nyman, D.Ogg, C.Persson, J.Sa P.Stenmark, M.Sundstrom, A.G.Thorsell, S.Van-Den-Berg, K.Wallde J.Weigelt, L.Holmberg-Schiavone, Structural Genomics Consorti
compound source
Molecule: Cystathionine Gamma-Lyase
Chain: A, B, C, D
Fragment: Residues 1-402
Synonym: Gamma-Cystathionase
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cth
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl-21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Bsa4
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.780 107.570 153.310 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand PLP enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S., Sun Q, Collins R, Huang S, Holmberg-Schiavone L, Anand GS, Tan CH, van-den-Berg S, Deng LW, Moore PK, Karlberg T, Sivaraman J, J Biol Chem. 2009 Jan 30;284(5):3076-85. Epub 2008 Nov 19. PMID:19019829
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk]
  • Biological Unit Coordinates (2nmp.pdb1.gz) 240 Kb
  • LPC: Ligand-Protein Contacts for 2NMP
  • CSU: Contacts of Structural Units for 2NMP
  • Likely Quarternary Molecular Structure file(s) for 2NMP
  • Structure Factors (450 Kb)
  • Retrieve 2NMP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NMP from S2C, [Save to disk]
  • Re-refined 2nmp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2NMP 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 2NMP
  • 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 2NMP, from MSDmotif at EBI
  • Fold representative 2nmp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nmp_C] [2nmp_A] [2nmp_B] [2nmp_D] [2nmp]
  • SWISS-PROT database: [P32929]
  • Domain organization of [CGL_HUMAN] by SWISSPFAM
  • Other resources with information on 2NMP
  • Community annotation for 2NMP 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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