3C6M Transferase date Feb 04, 2008
title Crystal Structure Of Human Spermine Synthase In Complex With Spermine And 5-Methylthioadenosine
authors J.Min, H.Wu, H.Zeng, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.E.Pegg, A.N.Plotnikov, Structural Genomics Consortium (Sgc)
compound source
Molecule: Spermine Synthase
Chain: A, B, C, D
Synonym: Spermidine Aminopropyltransferase, Spmsy
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sms
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a-Lic
symmetry Space Group: P 32
R_factor 0.209 R_Free 0.271
length a length b length c angle alpha angle beta angle gamma
88.262 88.262 197.668 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.45 Å
ligand MTA, SPM enzyme Transferase E.C. BRENDA
A, D, C, B

Primary referenceCrystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism., Wu H, Min J, Zeng H, McCloskey DE, Ikeguchi Y, Loppnau P, Michael AJ, Pegg AE, Plotnikov AN, J Biol Chem. 2008 Jun 6;283(23):16135-46. Epub 2008 Mar 26. PMID:18367445
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (215 Kb) [Save to disk]
  • Biological Unit Coordinates (3c6m.pdb1.gz) 115 Kb
  • Biological Unit Coordinates (3c6m.pdb2.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 3C6M
  • CSU: Contacts of Structural Units for 3C6M
  • Likely Quarternary Molecular Structure file(s) for 3C6M
  • Structure Factors (950 Kb)
  • Retrieve 3C6M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C6M from S2C, [Save to disk]
  • Re-refined 3c6m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C6M 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 3C6M
  • 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 3C6M, from MSDmotif at EBI
  • Fold representative 3c6m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c6m_C] [3c6m_B] [3c6m_D] [3c6m] [3c6m_A]
  • SWISS-PROT database: [P52788]
  • Domain organization of [SPSY_HUMAN] by SWISSPFAM
  • Other resources with information on 3C6M
  • Community annotation for 3C6M 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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