1TOC Complex (Hydrolase Inhibitor) date Jul 20, 1996
title Structure Of Serine Proteinase
authors A.Van De Locht, R.Huber, W.Bode
compound source
Molecule: Thrombin
Chain: A, C, E, G
Ec: 3.4.21.5
Engineered: Yes
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Plasma
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pmd8a

Molecule: Thrombin
Chain: B, D, F, H
Ec: 3.4.21.5
Engineered: Yes

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Plasma
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pmd8a

Molecule: Ornithodorin
Chain: R, S, T, U
Engineered: Yes

Organism_scientific: Ornithodoros Moubata
Organism_taxid: 6938
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pmd8a
symmetry Space Group: P 1 21 1
R_factor 0.230 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.300 89.900 101.400 90.00 108.40 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand
enzyme Hydrolase E.C.3.4.21.5 BRENDA
note 1TOC is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


S, T, R, U
  • serine-type endopeptidase in...


  • Primary referenceThe ornithodorin-thrombin crystal structure, a key to the TAP enigma?, van de Locht A, Stubbs MT, Bode W, Friedrich T, Bollschweiler C, Hoffken W, Huber R, EMBO J 1996 Nov 15;15(22):6011-7. PMID:8947023
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (278 Kb) [Save to disk]
  • Biological Unit Coordinates (1toc.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (1toc.pdb2.gz) 71 Kb
  • Biological Unit Coordinates (1toc.pdb3.gz) 71 Kb
  • Biological Unit Coordinates (1toc.pdb4.gz) 71 Kb
  • CSU: Contacts of Structural Units for 1TOC
  • Likely Quarternary Molecular Structure file(s) for 1TOC
  • Retrieve 1TOC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TOC from S2C, [Save to disk]
  • View 1TOC 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 1TOC
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1TOC, from MSDmotif at EBI
  • Genome occurence of 1TOC's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1toc.1, region A:,B [Jmol] [rasmolscript] [script source]
        - Domain d1toc.2, region C:,D [Jmol] [rasmolscript] [script source]
        - Domain d1toc.3, region E:,F [Jmol] [rasmolscript] [script source]
        - Domain d1toc.4, region G:,H [Jmol] [rasmolscript] [script source]
        - Domain d1tocr1, region R:1A-56 [Jmol] [rasmolscript] [script source]
        - Domain d1tocr2, region R:57-119 [Jmol] [rasmolscript] [script source]
        - Domain d1tocs1, region S:1A-56 [Jmol] [rasmolscript] [script source]
        - Domain d1tocs2, region S:57-119 [Jmol] [rasmolscript] [script source]
        - Domain d1toct1, region T:1A-56 [Jmol] [rasmolscript] [script source]
        - Domain d1toct2, region T:57-119 [Jmol] [rasmolscript] [script source]
        - Domain d1tocu1, region U:1A-56 [Jmol] [rasmolscript] [script source]
        - Domain d1tocu2, region U:57-119 [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: [1toc_D] [1toc_E] [1toc_U] [1toc_C] [1toc_H] [1toc_R] [1toc_F] [1toc_S] [1toc_B] [1toc_A] [1toc] [1toc_G] [1toc_T]
  • SWISS-PROT database: [P56409] [P00735]
  • Domain organization of [ORNT_ORNMO] [THRB_BOVIN] by SWISSPFAM
  • Domains found in 1TOC: [KU] [Tryp_SPc ] by SMART
  • Other resources with information on 1TOC
  • Community annotation for 1TOC at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1TOC from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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