4BDV

CRYSTAL STRUCTURE OF A TRUNCATED B-DOMAIN HUMAN FACTOR VIII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evaluation of the Metal Binding Sites in a Recombinant Coagulation Factor Viii Identifies Two Sites with Unique Metal Binding Properties.

Svensson, L.A.Thim, L.Olsen, O.H.Nicolaisen, E.M.

(2013) Biol.Chem. 394: 761

  • DOI: 10.1515/hsz-2012-0298

  • PubMed Abstract: 
  • Coagulation factor VIII is a glycosylated, non-covalent heterodimer consisting of a heavy chain (A1-A2-B domains) and a light chain (A3-C1-C2 domains). The association of the chains, and the stability and function of the dimer depend on the presence ...

    Coagulation factor VIII is a glycosylated, non-covalent heterodimer consisting of a heavy chain (A1-A2-B domains) and a light chain (A3-C1-C2 domains). The association of the chains, and the stability and function of the dimer depend on the presence of metal ions. We applied X-ray fluorescence, X-ray crystallographic structure determination with anomalous signals at different wavelengths, and colorimetric measurements to evaluate the metal binding sites in a recombinant factor VIII molecule, turoctocog alfa. We identified a metal binding site in domain A3 dominated by Cu(+) binding and a site in domain A1 dominated by Zn(2+) binding.


    Organizational Affiliation

    Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark. AnSv@novonordisk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FACTOR VIIIA HEAVY CHAIN, 92 KDA ISOFORM, B DOMAIN
A
760Homo sapiensMutation(s): 0 
Gene Names: F8 (F8C)
Find proteins for P00451 (Homo sapiens)
Go to Gene View: F8
Go to UniProtKB:  P00451
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FACTOR VIIIA LIGHT CHAIN
B
685Homo sapiensMutation(s): 0 
Gene Names: F8 (F8C)
Find proteins for P00451 (Homo sapiens)
Go to Gene View: F8
Go to UniProtKB:  P00451
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU1
Query on CU1

Download SDF File 
Download CCD File 
B
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.162 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 133.840α = 90.00
b = 133.840β = 90.00
c = 355.810γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Data collection
  • Version 1.2: 2018-01-17
    Type: Data collection