1GI9 Blood Clotting, Hydrolase date Jan 22, 2001
title A Novel Serine Protease Inhibition Motif Involving A Multi-C Short Hydrogen Bonding Network At The Active Site
authors B.A.Katz, K.Elrod, C.Luong, M.Rice, R.L.Mackman, P.A.Sprengeler, J J.Hatayte, J.Janc, J.Link, J.Litvak, R.Rai, K.Rice, S.Sideris, E.V W.Young
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: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic9lmwupa
Other_details: Chem.Biol. 7, 299-312, 2000

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: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic9lmwupa
Other_details: Chem.Biol. 7, 299-312, 2000
symmetry Space Group: C 1 2 1
R_factor 0.192 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.140 50.000 67.150 90.00 113.90 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand 123, CIT BindingDB enzyme Hydrolase E.C.3.4.21.73 BRENDA
related structures by homologous chain: 1EJN, 1GJ9
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceA novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site., Katz BA, Elrod K, Luong C, Rice MJ, Mackman RL, Sprengeler PA, Spencer J, Hataye J, Janc J, Link J, Litvak J, Rai R, Rice K, Sideris S, Verner E, Young W, J Mol Biol 2001 Apr 13;307(5):1451-86. PMID:11292354
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (1gi9.pdb1.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 1GI9
  • CSU: Contacts of Structural Units for 1GI9
  • Likely Quarternary Molecular Structure file(s) for 1GI9
  • Structure Factors (151 Kb)
  • Retrieve 1GI9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GI9 from S2C, [Save to disk]
  • Re-refined 1gi9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GI9 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 1GI9
  • 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 1GI9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gi9.1, 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: [1gi9_B] [1gi9_A] [1gi9]
  • SWISS-PROT database: [P00749]
  • Domain organization of [UROK_HUMAN] by SWISSPFAM
  • Domain found in 1GI9: [Tryp_SPc ] by SMART
  • Other resources with information on 1GI9
  • Community annotation for 1GI9 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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