1FNS Immune System date Aug 23, 2000
title Crystal Structure Of The Von Willebrand Factor (Vwf) A1 Doma Mutant In Complex With The Function Blocking Fab Nmc4
authors K.I.Varughese
compound source
Molecule: Immunoglobulin Nmc-4 Igg1
Chain: L
Fragment: Fab Fragment, Light Chain
 Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Cell: Hybridoma Cells, Mopc21 Cells

Molecule: Immunoglobulin Nmc-4 Igg1
Chain: H
Fragment: Fab Fragment, Heavy Chain
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Cell: Hybridoma Cells, Mopc21 Cells

Molecule: Von Willebrand Factor
Chain: A
Fragment: A1 Domain Residues 507 - 702, Or Glycoprotein Iba
(A\: Alpha) Binding Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: T7 Promoter
Expression_system_plasmid: Pet8c
symmetry Space Group: C 1 2 1
R_factor 0.172 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
209.396 62.673 73.789 90.00 108.88 90.00
method X-Ray Diffractionresolution 2.00 Å
related structures by homologous chain: 1A7P, 1A7R, 1CR9, 1IJB, 1OAK, 1SBS, 1T3F
Gene
Ontology
ChainFunctionProcessComponent
L


Primary referencevon Willebrand factor conformation and adhesive function is modulated by an internalized water molecule., Celikel R, Ruggeri ZM, Varughese KI, Nat Struct Biol 2000 Oct;7(10):881-4. PMID:11017197
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (1fns.pdb1.gz) 113 Kb
  • CSU: Contacts of Structural Units for 1FNS
  • Likely Quarternary Molecular Structure file(s) for 1FNS
  • Retrieve 1FNS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1FNS from S2C, [Save to disk]
    • View 1FNS 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 1FNS
  • 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 1FNS, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1fnsa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1fnsh1, region H:215-336 [Jmol] [rasmolscript] [script source]
        - Domain d1fnsh2, region H:337-439 [Jmol] [rasmolscript] [script source]
        - Domain d1fnsl1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1fnsl2, region L:108-214 [Jmol] [rasmolscript] [script source]
  • Fold representative 1fns 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: [1fns_A] [1fns] [1fns_L] [1fns_H]
  • SWISS-PROT database: [P01837] [P04275]
  • Domain organization of [IGKC_MOUSE] [VWF_HUMAN] by SWISSPFAM
  • Domains found in 1FNS: [IG_like] [IGv] [VWA ] by SMART
  • Alignments of the sequence of 1FNS with the sequences similar proteins can be viewed for 1FNS'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 1FNS
  • Community annotation for 1FNS 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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