7AHV | pdb_00007ahv

Anti-FIXa Fab of mim8 in complex with human FIXa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 
    0.283 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7AHV

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

A factor VIIIa-mimetic bispecific antibody, Mim8, ameliorates bleeding upon severe vascular challenge in hemophilia A mice.

Ostergaard, H.Lund, J.Greisen, P.J.Kjellev, S.Henriksen, A.Lorenzen, N.Johansson, E.Roder, G.Rasch, M.G.Johnsen, L.B.Egebjerg, T.Lund, S.Rahbek-Nielsen, H.Gandhi, P.S.Lamberth, K.Loftager, M.Andersen, L.M.Bonde, A.C.Stavenuiter, F.Madsen, D.E.Li, X.Holm, T.L.Ley, C.D.Thygesen, P.Zhu, H.Zhou, R.Thorn, K.Yang, Z.Hermit, M.B.Bjelke, J.R.Hansen, B.G.Hilden, I.

(2021) Blood 138: 1258-1268

  • DOI: https://doi.org/10.1182/blood.2020010331
  • Primary Citation Related Structures: 
    7AHU, 7AHV

  • PubMed Abstract: 

    Hemophilia A is a bleeding disorder resulting from deficient factor VIII (FVIII), which normally functions as a cofactor to activated factor IX (FIXa) that facilitates activation of factor X (FX). To mimic this property in a bispecific antibody format, a screening was conducted to identify functional pairs of anti-FIXa and anti-FX antibodies, followed by optimization of functional and biophysical properties. The resulting bispecific antibody (Mim8) assembled efficiently with FIXa and FX on membranes, and supported activation with an apparent equilibrium dissociation constant of 16 nM. Binding affinity with FIXa and FX in solution was much lower, with equilibrium dissociation constant values for FIXa and FX of 2.3 and 1.5 µM, respectively. In addition, the activity of Mim8 was dependent on stimulatory activity contributed by the anti-FIXa arm, which enhanced the proteolytic activity of FIXa by 4 orders of magnitude. In hemophilia A plasma and whole blood, Mim8 normalized thrombin generation and clot formation, with potencies 13 and 18 times higher than a sequence-identical analogue of emicizumab. A similar potency difference was observed in a tail vein transection model in hemophilia A mice, whereas reduction of bleeding in a severe tail-clip model was observed only for Mim8. Furthermore, the pharmacokinetic parameters of Mim8 were investigated and a half-life of 14 days shown in cynomolgus monkeys. In conclusion, Mim8 is an activated FVIII mimetic with a potent and efficacious hemostatic effect based on preclinical data.


  • Organizational Affiliation
    • Global Drug Discovery and.

Macromolecule Content 

  • Total Structure Weight: 82.39 kDa 
  • Atom Count: 5,700 
  • Modeled Residue Count: 726 
  • Deposited Residue Count: 732 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-FIXa Fab of mim8 heavy chain224Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-FIXa Fab of mim8 light chain214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor IXC [auth L]59Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens)
Explore P00740 
Go to UniProtKB:  P00740
PHAROS:  P00740
GTEx:  ENSG00000101981 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00740
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor IXD [auth H]235Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens)
Explore P00740 
Go to UniProtKB:  P00740
PHAROS:  P00740
GTEx:  ENSG00000101981 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00740
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0GJ

Query on 0GJ



Download:Ideal Coordinates CCD File
O [auth H]L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide
C14 H28 Cl N6 O5
XELWNHKFCNMWQO-LPEHRKFASA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth L],
P [auth H],
Q [auth H],
R [auth H],
S [auth H],
T [auth H],
U [auth H],
V [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
W [auth H]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free:  0.283 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.03α = 90
b = 97.03β = 90
c = 254.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-10-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary