1DAN Hydrolase Hydrolase Inhibitor date Mar 05, 1997
title Complex Of Active Site Inhibited Human Blood Coagulation Fac With Human Recombinant Soluble Tissue Factor
authors D.W.Banner
compound source
Molecule: Blood Coagulation Factor Viia Light Chain
Chain: L
Ec: 3.4.21.21
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Baby Hamster Kidney Cells
Organ: Blood
Expression_system: Mesocricetus Auratus
Expression_system_common: Golden Hamster
Expression_system_taxid: 10036
Expression_system_cell_line: Bhk Cells

Molecule: Blood Coagulation Factor Viia Heavy Chain
Chain: H
Ec: 3.4.21.21
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Baby Hamster Kidney Cells
Organ: Blood
Expression_system: Mesocricetus Auratus
Expression_system_common: Golden Hamster
Expression_system_taxid: 10036
Expression_system_cell_line: Bhk Cells

Molecule: Soluble Tissue Factor
Chain: T
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Baby Hamster Kidney Cells
Organ: Blood
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Soluble Tissue Factor
Chain: U
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Baby Hamster Kidney Cells
Organ: Blood
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.187 R_Free 0.218
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.650 82.550 126.500 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 0Z6, BGC, CA, CAC, CGU, CH2, CL, DPN, FUC enzyme Hydrolase E.C.3.4.21.21 BRENDA
note 1DAN (Molecule of the Month:pdb75)
related structures by homologous chain: 1JPS, 1KLI, 1YGC, 1Z6J
subcellular loc. Membrane localization by OPM: Eukaryotic plasma membrane
extracellular side
cytoplasmic side
Primary referenceThe crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor., Banner DW, D'Arcy A, Chene C, Winkler FK, Guha A, Konigsberg WH, Nemerson Y, Kirchhofer D, Nature 1996 Mar 7;380(6569):41-6. PMID:8598903
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (1dan.pdb1.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 1DAN
  • CSU: Contacts of Structural Units for 1DAN
  • Likely Quarternary Molecular Structure file(s) for 1DAN
  • Structure Factors (451 Kb)
  • Retrieve 1DAN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DAN from S2C, [Save to disk]
  • Re-refined 1dan structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DAN 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 1DAN
  • 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 1DAN, from MSDmotif at EBI
  • Genome occurence of 1DAN's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1danh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1danl3, region L:1-48 [Jmol] [rasmolscript] [script source]
        - Domain d1danl1, region L:49-86 [Jmol] [rasmolscript] [script source]
        - Domain d1danl2, region L:87-142 [Jmol] [rasmolscript] [script source]
        - Domain d1dan.1, region T:,U:91-106 [Jmol] [rasmolscript] [script source]
        - Domain d1danu1, region U:107-210 [Jmol] [rasmolscript] [script source]
  • Fold representative 1dan 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: [1dan_H] [1dan_T] [1dan_L] [1dan_U] [1dan_C] [1dan]
  • SWISS-PROT database: [P08709] [P13726]
  • Domain organization of [FA7_HUMAN] [TF_HUMAN] by SWISSPFAM
  • Domains found in 1DAN: [EGF] [EGF_CA] [GLA] [Tryp_SPc ] by SMART
  • Alignments of the sequence of 1DAN with the sequences similar proteins can be viewed for 1DAN's classification [FA7_HUMAN] [TF_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [FA7_HUMAN] [TF_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1DAN
  • Community annotation for 1DAN at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1DAN from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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