2HD1 Hydrolase date Jun 19, 2006
title Crystal Structure Of Pde9 In Complex With Ibmx
authors Q.Huai, H.Wang, W.Zhang, R.W.Colman, H.Robinson, H.Ke
compound source
Molecule: Phosphodiesterase 9a
Chain: A, B
Fragment: Catalytic Domain (Residues 181-506)
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 41 21 2
R_factor 0.215 R_Free 0.231
length a length b length c angle alpha angle beta angle gamma
103.513 103.513 269.727 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.23 Å
ligand IBM, MG, ZN BindingDB enzyme
note 2HD1 supersedes 1TBM
A, B

Primary referenceCrystal structure of phosphodiesterase 9 shows orientation variation of inhibitor 3-isobutyl-1-methylxanthine binding., Huai Q, Wang H, Zhang W, Colman RW, Robinson H, Ke H, Proc Natl Acad Sci U S A 2004 Jun 29;101(26):9624-9. Epub 2004 Jun 21. PMID:15210993
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (2hd1.pdb1.gz) 57 Kb
  • Biological Unit Coordinates (2hd1.pdb2.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 2HD1
  • CSU: Contacts of Structural Units for 2HD1
  • Likely Quarternary Molecular Structure file(s) for 2HD1
  • Structure Factors (911 Kb)
  • Retrieve 2HD1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HD1 from S2C, [Save to disk]
  • Re-refined 2hd1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2HD1 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 2HD1
  • 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 2HD1, from MSDmotif at EBI
  • Fold representative 2hd1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hd1_B] [2hd1_A] [2hd1]
  • SWISS-PROT database: [O76083]
  • Domain organization of [PDE9A_HUMAN] by SWISSPFAM
  • Domain found in 2HD1: [HDc ] by SMART
  • Other resources with information on 2HD1
  • Community annotation for 2HD1 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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