1TB7 Hydrolase date May 19, 2004
title Catalytic Domain Of Human Phosphodiesterase 4d In Complex Wi
authors K.Y.J.Zhang, G.L.Card, Y.Suzuki, D.R.Artis, D.Fong, S.Gillette, D. J.Neiman, B.L.West, C.Zhang, M.V.Milburn, S.H.Kim, J.Schlessing G.Bollag
compound source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d
Chain: A, B
Fragment: Catalytic Domain
Synonym: Dpde3, Pde43
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codon Plus(Ril)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.179 R_Free 0.192
length a length b length c angle alpha angle beta angle gamma
60.316 78.958 164.740 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.63 Å
ligand AMP, B3P, EDO, MG, ZN enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1TBB, 1Y2C
A, B

Primary referencecA Glutamine Switch Mechanism for Nucleotide Selectivity by Phosphodiesterases., Zhang KY, Card GL, Suzuki Y, Artis DR, Fong D, Gillette S, Hsieh D, Neiman J, West BL, Zhang C, Milburn MV, Kim SH, Schlessinger J, Bollag G, Mol Cell 2004 Jul 23;15(2):279-86. PMID:15260978
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (1tb7.pdb1.gz) 61 Kb
  • Biological Unit Coordinates (1tb7.pdb2.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 1TB7
  • CSU: Contacts of Structural Units for 1TB7
  • Likely Quarternary Molecular Structure file(s) for 1TB7
  • Structure Factors (661 Kb)
  • Retrieve 1TB7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TB7 from S2C, [Save to disk]
  • Re-refined 1tb7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1TB7 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 1TB7
  • 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 1TB7, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tb7a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1tb7b_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1tb7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1tb7_B] [1tb7_A] [1tb7]
  • SWISS-PROT database: [Q08499]
  • Domain organization of [PDE4D_HUMAN] by SWISSPFAM
  • Domain found in 1TB7: [HDc ] by SMART
  • Other resources with information on 1TB7
  • Community annotation for 1TB7 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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