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 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    4BDV

  • 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 of m ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FACTOR VIIIA HEAVY CHAIN, 92 KDA ISOFORM, B DOMAIN A760Homo sapiensMutation(s): 0 
Gene Names: F8F8C
Find proteins for P00451 (Homo sapiens)
Explore P00451 
Go to UniProtKB:  P00451
NIH Common Fund Data Resources
PHAROS:  P00451
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FACTOR VIIIA LIGHT CHAIN B685Homo sapiensMutation(s): 0 
Gene Names: F8F8C
Find proteins for P00451 (Homo sapiens)
Explore P00451 
Go to UniProtKB:  P00451
NIH Common Fund Data Resources
PHAROS:  P00451
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
5 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
B
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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 
  • R-Value Observed: 0.166 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.84α = 90
b = 133.84β = 90
c = 355.81γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Data collection
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary