2O05 Transferase date Nov 27, 2006
title Human Spermidine Synthase
authors J.Min, H.Wu, H.Zeng, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.N.Plotnikov, Structural Genomics Consortium (Sgc)
compound source
Molecule: Spermidine Synthase
Chain: A, B
Synonym: Putrescine Aminopropyltransferase, Spdsy
Ec: 2.5.1.16
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Srm, Sps1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.191 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.931 60.529 86.641 90.00 108.42 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MTA enzyme Transferase E.C.2.5.1.16 BRENDA
note 2O05 supersedes 1ZDZ
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure and mechanism of spermidine synthases., Wu H, Min J, Ikeguchi Y, Zeng H, Dong A, Loppnau P, Pegg AE, Plotnikov AN, Biochemistry. 2007 Jul 17;46(28):8331-9. Epub 2007 Jun 22. PMID:17585781
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (2o05.pdb1.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 2O05
  • CSU: Contacts of Structural Units for 2O05
  • Likely Quarternary Molecular Structure file(s) for 2O05
  • Structure Factors (574 Kb)
  • Retrieve 2O05 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2O05 from S2C, [Save to disk]
  • Re-refined 2o05 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2O05 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 2O05
  • 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 2O05, from MSDmotif at EBI
  • Fold representative 2o05 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2o05_B] [2o05_A] [2o05]
  • SWISS-PROT database: [P19623]
  • Domain organization of [SPEE_HUMAN] by SWISSPFAM
  • Other resources with information on 2O05
  • Community annotation for 2O05 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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