1DVM Blood Clotting date Jan 21, 2000
title Active Form Of Human Pai-1
authors T.J.Stout, H.Graham, D.I.Buckley, D.J.Matthews
compound source
Molecule: Plasminogen Activator Inhibitor-1
Chain: A, B, C, D
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Umbilical Vein Endothelium Library
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptrchis2a
symmetry Space Group: P 1
R_factor 0.218 R_Free 0.292
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.764 74.674 103.445 85.19 86.17 64.34
method X-Ray Diffractionresolution 2.40 Å
ligand CL enzyme
related structures by homologous chain: 1C5G, 1OC0
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • negative regulation of endop...
  • negative regulation of smoot...

  • Primary referenceStructures of active and latent PAI-1: a possible stabilizing role for chloride ions., Stout TJ, Graham H, Buckley DI, Matthews DJ, Biochemistry 2000 Jul 25;39(29):8460-9. PMID:10913251
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (277 Kb) [Save to disk]
  • Biological Unit Coordinates (1dvm.pdb1.gz) 72 Kb
  • Biological Unit Coordinates (1dvm.pdb2.gz) 70 Kb
  • Biological Unit Coordinates (1dvm.pdb3.gz) 68 Kb
  • Biological Unit Coordinates (1dvm.pdb4.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 1DVM
  • CSU: Contacts of Structural Units for 1DVM
  • Likely Quarternary Molecular Structure file(s) for 1DVM
  • Structure Factors (529 Kb)
  • Retrieve 1DVM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DVM from S2C, [Save to disk]
  • Re-refined 1dvm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DVM 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 1DVM
  • 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 1DVM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dvma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dvmb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1dvmc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1dvmd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1dvm 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: [1dvm_C] [1dvm] [1dvm_A] [1dvm_D] [1dvm_B]
  • SWISS-PROT database: [P05121]
  • Domain organization of [PAI1_HUMAN] by SWISSPFAM
  • Domain found in 1DVM: [SERPIN ] by SMART
  • Alignments of the sequence of 1DVM with the sequences similar proteins can be viewed for 1DVM's classification [PAI1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [PAI1_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1DVM
  • Community annotation for 1DVM 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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