1FE8 Immune System date Jul 21, 2000
title Crystal Structure Of The Von Willebrand Factor A3 Domain In With A Fab Fragment Of Igg Ru5 That Inhibits Collagen Bindi
authors B.Bouma, E.G.Huizinga, M.E.Schiphorst, J.J.Sixma, J.Kroon, P.Gros
compound source
Molecule: Von Willebrand Factor
Chain: A, B, C
Fragment: Collagen Binding Domain A3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Immunoglobulin Igg Ru5
Chain: H, I, J
Fragment: Fab Fragment Heavy Chain

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Immunoglobulin Igg Ru5
Chain: L, M, N
Fragment: Fab Fragment Light Chain

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
symmetry Space Group: C 1 2 1
R_factor 0.227 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.800 183.600 131.800 90.00 116.20 90.00
method X-Ray Diffractionresolution 2.03 Å
ligand CAC, FUC, MSE, NAG enzyme
related structures by homologous chain: 1AO3, 1ATZ, 1H0D, 1KIP, 1UB5, 1UZ6
Gene
Ontology
ChainFunctionProcessComponent
M, N, L


Primary referenceIdentification of the collagen-binding site of the von Willebrand factor A3-domain., Romijn RA, Bouma B, Wuyster W, Gros P, Kroon J, Sixma JJ, Huizinga EG, J Biol Chem 2001 Mar 30;276(13):9985-91. PMID:11098050
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (307 Kb) [Save to disk]
  • Biological Unit Coordinates (1fe8.pdb1.gz) 106 Kb
  • Biological Unit Coordinates (1fe8.pdb2.gz) 105 Kb
  • Biological Unit Coordinates (1fe8.pdb3.gz) 103 Kb
  • Biological Unit Coordinates (1fe8.pdb4.gz) 593 Kb
  • LPC: Ligand-Protein Contacts for 1FE8
  • CSU: Contacts of Structural Units for 1FE8
  • Likely Quarternary Molecular Structure file(s) for 1FE8
  • Structure Factors (1593 Kb)
  • Retrieve 1FE8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1FE8 from S2C, [Save to disk]
  • Re-refined 1fe8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1FE8 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 1FE8
  • 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 1FE8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1fe8a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1fe8b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1fe8c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1fe8h1, region H:1-115 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8h2, region H:116-216 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8i1, region I:1-115 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8i2, region I:116-216 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8j1, region J:1-115 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8j2, region J:116-216 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8l1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8l2, region L:108-211 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8m1, region M:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8m2, region M:108-211 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8n1, region N:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1fe8n2, region N:108-211 [Jmol] [rasmolscript] [script source]
  • Fold representative 1fe8 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: [1fe8_A] [1fe8_B] [1fe8_C] [1fe8_L] [1fe8_H] [1fe8] [1fe8_M] [1fe8_J] [1fe8_I] [1fe8_N]
  • SWISS-PROT database: [P01837] [P04275]
  • Domain organization of [IGKC_MOUSE] [VWF_HUMAN] by SWISSPFAM
  • Domains found in 1FE8: [IG_like] [IGv] [VWA ] by SMART
  • Alignments of the sequence of 1FE8 with the sequences similar proteins can be viewed for 1FE8's classification [IGKC_MOUSE] [VWF_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 [IGKC_MOUSE] [VWF_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1FE8
  • Community annotation for 1FE8 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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