1PPB THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT date
authors Bode, W.
compound source
symmetry
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.92
ligand 0G6 enzyme
note 1PPB (Molecule of the Month:pdb25)
related structures by homologous chain: 1C1V, 1K22, 1SFQ, 1ZRB
Gene
Ontology
ChainFunctionProcessComponent
H


L


Primary referenceThe refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment., Bode W, Mayr I, Baumann U, Huber R, Stone SR, Hofsteenge J, EMBO J 1989 Nov;8(11):3467-75. PMID:2583108
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (1ppb.pdb1.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 1PPB
  • CSU: Contacts of Structural Units for 1PPB
  • Likely Quarternary Molecular Structure file(s) for 1PPB
  • Retrieve 1PPB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PPB from S2C, [Save to disk]
  • View 1PPB 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 1PPB
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1PPB, from MSDmotif at EBI
  • Genome occurence of 1PPB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ppb.1, region L:,H [Jmol] [rasmolscript] [script source]
  • Fold representative 1ppb 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: [1ppb_L] [1ppb_H] [1ppb] [1ppb_I]
  • SWISS-PROT database: [P00734]
  • Domain organization of [THRB_HUMAN] by SWISSPFAM
  • Domain found in 1PPB: [Tryp_SPc ] by SMART
  • Other resources with information on 1PPB
  • Community annotation for 1PPB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1PPB from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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