1RO6 Hydrolase date Dec 01, 2003
title Crystal Structure Of Pde4b2b Complexed With Rolipram (R & S)
authors R.X.Xu, W.J.Rocque, M.H.Lambert, D.E.Vanderwall, R.T.Nolte
compound source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4b
Chain: A, B
Fragment: Catalytic Domain
Synonym: Dpde4, Pde32, Pde4b2b
Ec: 3.1.4.17
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde4b
Expression_system: Unidentified Baculovirus
Expression_system_taxid: 10469
symmetry Space Group: C 2 2 21
R_factor 0.217 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.148 160.891 108.780 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ARS, MN, ROL, ZN BindingDB enzyme Hydrolase E.C.3.1.4.17 BRENDA
related structures by homologous chain: 1OYN, 1ROR
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structures of the catalytic domain of phosphodiesterase 4B complexed with AMP, 8-Br-AMP, and rolipram., Xu RX, Rocque WJ, Lambert MH, Vanderwall DE, Luther MA, Nolte RT, J Mol Biol. 2004 Mar 19;337(2):355-65. PMID:15003452
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (128 Kb) [Save to disk]
  • Biological Unit Coordinates (1ro6.pdb1.gz) 63 Kb
  • Biological Unit Coordinates (1ro6.pdb2.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 1RO6
  • CSU: Contacts of Structural Units for 1RO6
  • Likely Quarternary Molecular Structure file(s) for 1RO6
  • Structure Factors (537 Kb)
  • Retrieve 1RO6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RO6 from S2C, [Save to disk]
  • Re-refined 1ro6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RO6 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 1RO6
  • 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 1RO6, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ro6a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ro6b_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1ro6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ro6_B] [1ro6] [1ro6_A]
  • SWISS-PROT database: [Q07343]
  • Domain organization of [PDE4B_HUMAN] by SWISSPFAM
  • Domain found in 1RO6: [HDc ] by SMART
  • Other resources with information on 1RO6
  • Community annotation for 1RO6 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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