1O5D Blood Clotting, Hydrolase date Sep 09, 2003
title Dissecting And Designing Inhibitor Selectivity Determinants At The S1 Site Using An Artificial Ala190 Protease (Ala190 Upa)
authors B.A.Katz, C.Luong, J.D.Ho, J.R.Somoza, E.Gjerstad, J.Tang, S.R.Williams, E.Verner, R.L.Mackman, W.B.Young, P.A.Sprengeler, H.Chan, K.Mortara, J.W.Janc, M.E.Mcgrath
compound source
Molecule: Coagulation Factor Vii
Chain: L
Fragment: Light Chain
Synonym: Serum Prothrombin Conversion Accelerator, Eptacog Alfa;
Ec: 3.4.21.21
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F7
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: 293
Expression_system_organ: Embryonic Kidney
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pci-Neo(Promega)

Molecule: Coagulation Factor Vii
Chain: H
Fragment: Heavy Chain (Catalytic Domain)
Synonym: Serum Prothrombin Conversion Accelerator, Eptacog Alfa;
Ec: 3.4.21.21
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F7
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: 293
Expression_system_organ: Embryonic Kidney
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pci-Neo(Promega)

Molecule: Tissue Factor
Chain: T
Synonym: Tf, Coagulation Factor III, Thromboplastin, Cd142 Antigen;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Des3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-21a(+)
Other_details: Escherichia Coli
symmetry Space Group: P 1 21 1
R_factor 0.226 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.540 69.030 79.120 90.00 89.99 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand CR9 enzyme Hydrolase E.C.3.4.21.21 BRENDA
related structures by homologous chain: 1FAK, 1JBU, 1UJ3, 1Z6J
Gene
Ontology
ChainFunctionProcessComponent
H


L


T


Primary referenceDissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA)., Katz BA, Luong C, Ho JD, Somoza JR, Gjerstad E, Tang J, Williams SR, Verner E, Mackman RL, Young WB, Sprengeler PA, Chan H, Mortara K, Janc JW, McGrath ME, J Mol Biol 2004 Nov 19;344(2):527-47. PMID:15522303
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (201 Kb) [Save to disk]
  • Biological Unit Coordinates (1o5d.pdb1.gz) 194 Kb
  • LPC: Ligand-Protein Contacts for 1O5D
  • CSU: Contacts of Structural Units for 1O5D
  • Likely Quarternary Molecular Structure file(s) for 1O5D
  • Structure Factors (338 Kb)
  • Retrieve 1O5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1O5D from S2C, [Save to disk]
  • Re-refined 1o5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1O5D 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 1O5D
  • 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 1O5D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o5dh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1o5dl1, region L:47-86 [Jmol] [rasmolscript] [script source]
        - Domain d1o5dl2, region L:87-142 [Jmol] [rasmolscript] [script source]
        - Domain d1o5dt2, region T:107-205 [Jmol] [rasmolscript] [script source]
        - Domain d1o5dt1, region T:6-106 [Jmol] [rasmolscript] [script source]
  • Fold representative 1o5d 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: [1o5d] [1o5d_T] [1o5d_L] [1o5d_H]
  • SWISS-PROT database: [P08709] [P13726]
  • Domain organization of [FA7_HUMAN] [TF_HUMAN] by SWISSPFAM
  • Domains found in 1O5D: [EGF] [EGF_CA] [GLA] [Tryp_SPc ] by SMART
  • Other resources with information on 1O5D
  • Community annotation for 1O5D 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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