Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 175945.94 
• Atom Count: 10034 
• Residue Count: 1512 
• Unique protein chains: 1

6MF2

Improved Model of Human Coagulation Factor VIII

• DOI: 10.2210/pdb6MF2/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus


• Deposited: 2018-09-08 Released: 2019-09-11 
• Deposition Author(s): Smith, I.W., Spiegel, P.C.

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Experimental Data Snapshot

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

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. --: --

• PubMed: 31454152 
• DOI: 10.1111/jth.14621
• Primary Citation of Related Structures:  
  6MF0


• 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) 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.

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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




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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
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor VIII	A	1512	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU1	A	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 134.569	α = 90.00
b = 134.569	β = 90.00
c = 359.496	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing
PHENIX	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-09-08 
• Released Date: 2019-09-11 
• Deposition Author(s): Smith, I.W., Spiegel, P.C.

Revision History 

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