6MF2

Improved Model of Human Coagulation Factor VIII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60936 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The 3.2 angstrom Structure of a Bioengineered Variant of Blood Coagulation Factor VIII Indicates Two Conformations of the C2 Domain.

Smith, I.W.d'Aquino, A.E.Coyle, C.W.Fedanov, A.Parker, E.T.Denning, G.Spencer, H.T.Lollar, P.Doering, C.B.Spiegel Jr., P.C.

(2019) J.Thromb.Haemost. --: --

  • DOI: 10.1111/jth.14621
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Coagulation factor VIII represents one of the oldest protein-based therapeutics, serving as an effective hemophilia A treatment for half a century. Optimal treatment consists of repeated intravenous infusions of blood coagulation factor VIII (FVIII) ...

    Coagulation factor VIII represents one of the oldest protein-based therapeutics, serving as an effective hemophilia A treatment for half a century. Optimal treatment consists of repeated intravenous infusions of blood coagulation factor VIII (FVIII) per week for life. Despite overall treatment success, significant limitations remain including treatment invasiveness, duration, immunogenicity, and cost. These issues have inspired research into the development of bioengineered FVIII products and gene therapies.


    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V.,Grosse-Kunstleve, R.W.,Echols, N.,Headd, J.J.,Moriarty, N.W.,Mustyakimov, M.,Terwilliger, T.C.,Urzhumtsev, A.,Zwart, P.H.,Adams, P.D.
      (2012) Acta Crystallogr. D Biol. Crystallogr. 68: 352
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D.,Afonine, P.V.,Bunkoczi, G.,Chen, V.B.,Davis, I.W.,Echols, N.,Headd, J.J.,Hung, L.W.,Kapral, G.J.,Grosse-Kunstleve, R.W.,McCoy, A.J.,Moriarty, N.W.,Oeffner, R.,Read, R.J.,Richardson, D.C.,Richardson, J.S.,Terwilliger, T.C.,Zwart, P.H.
      (2010) Acta Crystallogr. D Biol. Crystallogr. 66: 213


    Organizational Affiliation

    Department of Chemistry, Western Washington University, 516 High Street MS 9150,, Bellingham, WA, 98225-9150.,Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University, Atlanta, GA, 30322.,Graduate Program in Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA, 30322.,Expression Therapeutics, LLC. Tucker, GA, 30084.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VIII
A
1512Homo 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 5 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 
A
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
BMA
Query on BMA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60936 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.252 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 134.569α = 90.00
b = 134.569β = 90.00
c = 359.496γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release