1FZD Blood Coagulation date Jun 22, 1998
title Structure Of Recombinant Alphaec Domain From Human Fibrinoge
authors G.Spraggon, D.Applegate, S.J.Everse, J.Z.Zhang, L.Veerapandian, R.F.Doolittle, G.Grieninger
compound source
Molecule: Fibrinogen-420
Chain: A, B, C, D, E, F, G, H
Fragment: Alpha-Ec Domain
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Blood
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
symmetry Space Group: P 1
R_factor 0.195 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.250 105.180 71.140 104.60 108.95 71.47
method X-Ray Diffractionresolution 2.10 Å
ligand CA, MAN, NAG, NDG enzyme
Primary referenceCrystal structure of a recombinant alphaEC domain from human fibrinogen-420., Spraggon G, Applegate D, Everse SJ, Zhang JZ, Veerapandian L, Redman C, Doolittle RF, Grieninger G, Proc Natl Acad Sci U S A 1998 Aug 4;95(16):9099-104. PMID:9689040
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (286 Kb) [Save to disk]
  • Biological Unit Coordinates (1fzd.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (1fzd.pdb2.gz) 138 Kb
  • LPC: Ligand-Protein Contacts for 1FZD
  • CSU: Contacts of Structural Units for 1FZD
  • Likely Quarternary Molecular Structure file(s) for 1FZD
  • Retrieve 1FZD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1FZD from S2C, [Save to disk]
    • View 1FZD 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1FZD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1FZD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1fzda_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1fzdb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1fzdc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1fzdd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1fzde_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1fzdf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1fzdg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1fzdh_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1fzd 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: [1fzd_A] [1fzd_B] [1fzd_C] [1fzd_D] [1fzd_E] [1fzd_F] [1fzd_G] [1fzd_H]
  • SWISS-PROT database: [P02671]
  • Domain organization of [FIBA_HUMAN] by SWISSPFAM
  • Domain found in 1FZD: [FBG ] by SMART
  • Alignments of the sequence of 1FZD with the sequences similar proteins can be viewed for 1FZD's classification [FIBA_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 [FIBA_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1FZD
  • Community annotation for 1FZD 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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