2GDZ Oxidoreductase date Mar 17, 2006
title Crystal Structure Of 15-Hydroxyprostaglandin Dehydrogenase T Complexed With Nad+
authors E.S.Pilka, K.Guo, K.Kavanagh, F.Von Delft, C.Arrowsmith, J.Weigel A.Edwards, M.Sundstrom, U.Oppermann, Structural Genomics Conso (Sgc)
compound source
Molecule: Nad+-Dependent 15-Hydroxyprostaglandin Dehydrogen
Chain: A
Fragment: Residues (-1)-265
Synonym: 15 Hydroxyprostaglandin Dehydrogenase Type1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-R3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Sgc
symmetry Space Group: P 41 21 2
R_factor 0.176 R_Free 0.212
length a length b length c angle alpha angle beta angle gamma
49.540 49.540 195.771 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand NAD enzyme Oxidoreductase E.C. BRENDA

Primary referenceHigh-Affinity Inhibitors of Human NAD-Dependent 15-Hydroxyprostaglandin Dehydrogenase: Mechanisms of Inhibition and Structure-Activity Relationships., Niesen FH, Schultz L, Jadhav A, Bhatia C, Guo K, Maloney DJ, Pilka ES, Wang M, Oppermann U, Heightman TD, Simeonov A, PLoS One. 2010 Nov 2;5(11):e13719. PMID:21072165
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (2gdz.pdb1.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 2GDZ
  • CSU: Contacts of Structural Units for 2GDZ
  • Likely Quarternary Molecular Structure file(s) for 2GDZ
  • Structure Factors (1528 Kb)
  • Retrieve 2GDZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2GDZ from S2C, [Save to disk]
  • Re-refined 2gdz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2GDZ 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 2GDZ
  • 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 2GDZ, from MSDmotif at EBI
  • Fold representative 2gdz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2gdz] [2gdz_A]
  • SWISS-PROT database: [P15428]
  • Domain organization of [PGDH_HUMAN] by SWISSPFAM
  • Other resources with information on 2GDZ
  • Community annotation for 2GDZ 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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