1IMV Signaling Protein date May 11, 2001
title 2.85 A Crystal Structure Of Pedf
authors M.Simonovic, P.G.W.Gettins, K.Volz
compound source
Molecule: Pigment Epithelium-Derived Factor
Chain: A
Synonym: Pedf
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Bhk
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pma
symmetry Space Group: P 21 21 2
R_factor 0.188 R_Free 0.227
length a length b length c angle alpha angle beta angle gamma
176.174 62.514 45.406 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand NAG enzyme
  • serine-type endopeptidase in...

  • Primary referenceCrystal structure of human PEDF, a potent anti-angiogenic and neurite growth-promoting factor., Simonovic M, Gettins PG, Volz K, Proc Natl Acad Sci U S A 2001 Sep 25;98(20):11131-5. PMID:11562499
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1imv.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 1IMV
  • CSU: Contacts of Structural Units for 1IMV
  • Likely Quarternary Molecular Structure file(s) for 1IMV
  • Structure Factors (128 Kb)
  • Retrieve 1IMV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IMV from S2C, [Save to disk]
  • Re-refined 1imv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1IMV 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 1IMV
  • 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 1IMV, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1imva_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1imv 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: [1imv_A] [1imv]
  • SWISS-PROT database: [P36955]
  • Domain organization of [PEDF_HUMAN] by SWISSPFAM
  • Domain found in 1IMV: [SERPIN ] by SMART
  • Other resources with information on 1IMV
  • Community annotation for 1IMV 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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