1GJD Blood Clotting, Hydrolase date May 03, 2001
title Engineering Inhibitors Highly Selective For The S1 Sites Of Trypsin-Like Serine Protease Drug Targets
authors B.A.Katz, P.A.Sprengeler, C.Luong, E.Verner, J.R.Spencer, J.G.Breitenbucher, H.Hui, D.Mcgee, D.Allen, A.Martelli, R.L.Mack
compound source
Molecule: Urokinase-Type Plasminogen Activator
Chain: A
Fragment: Short Chain
Synonym: Upa, U-Plasminogen Activator, Urokinase-Plasminoge Activator;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic9lmwupa
Other_details: P.Pastoris

Molecule: Urokinase-Type Plasminogen Activator
Chain: B
Fragment: Catalytic Domain
Synonym: Upa, U-Plasminogen Activator, Urokinase-Plasminoge Activator;
Ec: 3.4.21.73
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic9lmwupa
Other_details: P.Pastoris
symmetry Space Group: C 1 2 1
R_factor 0.180 R_Free 0.189
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.030 49.760 66.150 90.00 112.99 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand 136, CIT BindingDB enzyme Hydrolase E.C.3.4.21.73 BRENDA
related structures by homologous chain: 1C5X, 1GJC
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceEngineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets., Katz BA, Sprengeler PA, Luong C, Verner E, Elrod K, Kirtley M, Janc J, Spencer JR, Breitenbucher JG, Hui H, McGee D, Allen D, Martelli A, Mackman RL, Chem Biol 2001 Nov;8(11):1107-21. PMID:11731301
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (1gjd.pdb1.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 1GJD
  • CSU: Contacts of Structural Units for 1GJD
  • Likely Quarternary Molecular Structure file(s) for 1GJD
  • Structure Factors (111 Kb)
  • Retrieve 1GJD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GJD from S2C, [Save to disk]
  • Re-refined 1gjd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GJD 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 1GJD
  • 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 1GJD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gjd.1, region A:,B [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: [1gjd_B] [1gjd] [1gjd_A]
  • SWISS-PROT database: [P00749]
  • Domain organization of [UROK_HUMAN] by SWISSPFAM
  • Domain found in 1GJD: [Tryp_SPc ] by SMART
  • Other resources with information on 1GJD
  • Community annotation for 1GJD 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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