1QDM Hydrolase date May 19, 1999
title Crystal Structure Of Prophytepsin, A Zymogen Of A Barley Vacuolar Aspartic Proteinase.
authors J.Kervinen, G.J.Tobin, J.Costa, D.S.Waugh, A.Wlodawer, A.Zdanov
compound source
Molecule: Prophytepsin
Chain: A, B, C
Ec: 3.4.23.40
 Organism_scientific: Hordeum Vulgare
Organism_taxid: 4513
symmetry Space Group: P 1 21 1
R_factor 0.224 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.000 160.900 81.400 90.00 109.60 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand
enzyme Hydrolase E.C.3.4.23.40 BRENDA
related structures by homologous chain: 1B5F, 1LYB
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceCrystal structure of plant aspartic proteinase prophytepsin: inactivation and vacuolar targeting., Kervinen J, Tobin GJ, Costa J, Waugh DS, Wlodawer A, Zdanov A, EMBO J 1999 Jul 15;18(14):3947-55. PMID:10406799
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (194 Kb) [Save to disk]
  • Biological Unit Coordinates (1qdm.pdb1.gz) 65 Kb
  • Biological Unit Coordinates (1qdm.pdb2.gz) 65 Kb
  • Biological Unit Coordinates (1qdm.pdb3.gz) 65 Kb
  • CSU: Contacts of Structural Units for 1QDM
  • Likely Quarternary Molecular Structure file(s) for 1QDM
  • Structure Factors (407 Kb)
  • Retrieve 1QDM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QDM from S2C, [Save to disk]
  • Re-refined 1qdm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1QDM 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 1QDM
  • 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
  • 3D motif for 1QDM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qdma1, region A:1S-104S [Jmol] [rasmolscript] [script source]
        - Domain d1qdma2, region A:2-247,A:248-338 [Jmol] [rasmolscript] [script source]
        - Domain d1qdmb1, region B:1S-104S [Jmol] [rasmolscript] [script source]
        - Domain d1qdmb2, region B:2-247,B:248-338 [Jmol] [rasmolscript] [script source]
        - Domain d1qdmc1, region C:1S-104S [Jmol] [rasmolscript] [script source]
        - Domain d1qdmc2, region C:3-247,C:248-338 [Jmol] [rasmolscript] [script source]
  • 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: [1qdm] [1qdm_C] [1qdm_A] [1qdm_B]
  • SWISS-PROT database: [P42210]
  • Domain organization of [ASPR_HORVU] by SWISSPFAM
  • Domain found in 1QDM: [SapB ] by SMART
    • Other resources with information on 1QDM
  • Community annotation for 1QDM 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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