1I7M Lyase date Mar 09, 2001
title Human S-Adenosylmethionine Decarboxylase With Covalently Bou Pyruvoyl Group And Complexed With 4-Amidinoindan-1-One-2'- Amidinohydrazone
authors W.D.Tolbert, J.L.Ekstrom, I.I.Mathews, J.A.Secrist Iii, A.E.Pegg S.E.Ealick
compound source
Molecule: S-Adenosylmethionine Decarboxylase Beta Chain
Chain: B, D
Ec: 4.1.1.50
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: S-Adenosylmethionine Decarboxylase Alpha Chain
Chain: A, C
Ec: 4.1.1.50
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.242 R_Free 0.294
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.899 55.672 96.086 90.00 110.39 90.00
method X-Ray Diffractionresolution 2.24 Å
ligand CG, MSE, PUT, PYR enzyme Lyase E.C.4.1.1.50 BRENDA
related structures by homologous chain: 1I79, 1JEN
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceThe structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase., Tolbert WD, Ekstrom JL, Mathews II, Secrist JA 3rd, Kapoor P, Pegg AE, Ealick SE, Biochemistry 2001 Aug 14;40(32):9484-94. PMID:11583147
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (1i7m.pdb1.gz) 107 Kb
  • Biological Unit Coordinates (1i7m.pdb2.gz) 55 Kb
  • Biological Unit Coordinates (1i7m.pdb3.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 1I7M
  • CSU: Contacts of Structural Units for 1I7M
  • Likely Quarternary Molecular Structure file(s) for 1I7M
  • Structure Factors (554 Kb)
  • Retrieve 1I7M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1I7M from S2C, [Save to disk]
  • Re-refined 1i7m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1I7M 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 1I7M
  • 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 1I7M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1i7m.1, region B:,A [Jmol] [rasmolscript] [script source]
        - Domain d1i7m.2, region D:,C [Jmol] [rasmolscript] [script source]
  • Fold representative 1i7m 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: [1i7m_D] [1i7m] [1i7m_B] [1i7m_C] [1i7m_A]
  • SWISS-PROT database: [P17707]
  • Domain organization of [DCAM_HUMAN] by SWISSPFAM
  • Other resources with information on 1I7M
  • Community annotation for 1I7M 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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