1TBF Hydrolase date May 20, 2004
title Catalytic Domain Of Human Phosphodiesterase 5a In Complex Wi Sildenafil
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: Cgmp-Specific 3',5'-Cyclic Phosphodiesterase
Chain: A
Fragment: Catalytic Domain
Synonym: Cgb-Pde, Cgmp-Binding Cgmp-Specific Phosphodiester
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde5a, Pde5
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 31 2 1
R_factor 0.157 R_Free 0.186
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.097 76.097 99.272 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.30 Å
ligand GOL, MG, VIA, ZN BindingDB enzyme Hydrolase E.C.3.1.4.17 BRENDA
related structures by homologous chain: 1XOZ
Gene
Ontology
ChainFunctionProcessComponent
A


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] (124 Kb) [Save to disk]
  • Biological Unit Coordinates (1tbf.pdb1.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 1TBF
  • CSU: Contacts of Structural Units for 1TBF
  • Likely Quarternary Molecular Structure file(s) for 1TBF
  • Structure Factors (549 Kb)
  • Retrieve 1TBF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TBF from S2C, [Save to disk]
  • Re-refined 1tbf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1TBF 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 1TBF
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1TBF from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1TBF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tbfa_, region A [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1tbf] [1tbf_A]
  • SWISS-PROT database: [O76074]
  • Domain organization of [PDE5A_HUMAN] by SWISSPFAM
  • Domain found in 1TBF: [HDc ] by SMART
  • Other resources with information on 1TBF
  • Community annotation for 1TBF 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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