1OAK Complex (Willebrand Immunoglobulin) date Dec 18, 1997
title Crystal Structure Of The Von Willebrand Factor (Vwf) A1 Domain In Complex With The Function Blocking Nmc-4 Fab
authors R.Celikel, K.I.Varughese
compound source
Molecule: Nmc-4 Igg1
Chain: L
Fragment: Fab Fragment, An Anti Von Willebrand Factor (Vwf) A1 Domain;
Engineered: Yes
Other_details: The Antibody Heavy Chain Consists Of Two Segments, H1 And H2, Both Labeled Chain H In This Entry;
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Cell_line: Hybridoma
Organ: Blood
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell_line: Mopc21

Molecule: Nmc-4 Igg1
Chain: H
Fragment: Fab Fragment, An Anti Von Willebrand Factor (Vwf) A1 Domain;
Engineered: Yes
Other_details: The Antibody Heavy Chain Consists Of Two Segments, H1 And H2, Both Labeled Chain H In This Entry;

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Cell_line: Hybridoma
Organ: Blood
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell_line: Mopc21

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
Organ: Blood
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 0.201 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
208.200 61.900 72.900 90.00 108.60 90.00
method X-Ray Diffractionresolution 2.20 Å
related structures by homologous chain: 1AUQ, 1FNS, 1KCU, 1YEE, 2CK0, 43C9
Gene
Ontology
ChainFunctionProcessComponent
L


Primary referenceCrystal structure of the von Willebrand factor A1 domain in complex with the function blocking NMC-4 Fab., Celikel R, Varughese KI, Madhusudan, Yoshioka A, Ware J, Ruggeri ZM, Nat Struct Biol 1998 Mar;5(3):189-94. PMID:9501911
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (1oak.pdb1.gz) 108 Kb
  • CSU: Contacts of Structural Units for 1OAK
  • Likely Quarternary Molecular Structure file(s) for 1OAK
  • Retrieve 1OAK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OAK from S2C, [Save to disk]
  • View 1OAK 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 1OAK
  • 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 1OAK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1oaka_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1oakh1, region H:215-336 [Jmol] [rasmolscript] [script source]
        - Domain d1oakh2, region H:337-437 [Jmol] [rasmolscript] [script source]
        - Domain d1oakl1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1oakl2, region L:108-212 [Jmol] [rasmolscript] [script source]
  • Fold representative 1oak 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: [1oak_H] [1oak_A] [1oak] [1oak_L]
  • SWISS-PROT database: [P01837] [P04275]
  • Domain organization of [IGKC_MOUSE] [VWF_HUMAN] by SWISSPFAM
  • Domains found in 1OAK: [IGc1] [IGv] [VWA ] by SMART
  • Alignments of the sequence of 1OAK with the sequences similar proteins can be viewed for 1OAK'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 1OAK
  • Community annotation for 1OAK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science