9QRV | pdb_00009qrv

Crystal Structure of an anti-VWF CK Domain Fab in Complex with the C-Terminal CK Domain of Cynomolgus Monkey von Willebrand Factor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.249 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

HMB-002: a monovalent antibody that elevates circulating VWF and FVIII levels for treatment of von Willebrand disease.

Hager, M.Zivkovic, M.Gandhi, P.S.Rasmussen, C.Bonvoisin, C.Harrison, R.A.Poulsen, E.Huskens, D.Roest, M.Ferrara, F.Naretto, A.Renaud, L.Olsen, O.H.Eskesen, N.O.Holten-Andersen, L.Malladi, R.Rea, C.J.Sorensen, B.Urbanus, R.T.Ostergaard, H.

(2026) Blood Adv 10: 2551-2562

  • DOI: https://doi.org/10.1182/bloodadvances.2025018516
  • Primary Citation Related Structures: 
    9QRV

  • PubMed Abstract: 

    Von Willebrand disease (VWD) is the most common inherited bleeding disorder, resulting from deficiency or dysfunction of von Willebrand factor (VWF), a protein crucial for hemostasis. Current prophylactic options present significant limitations including poor tolerability, short half-life, or the requirement for frequent IV administration. Here, we report HMB-002, a human Fc-silenced monovalent IgG4 antibody designed to provide convenient subcutaneous prophylaxis by binding and elevating levels of endogenous VWF. Binding studies and X-ray crystallography revealed that HMB-002 binds VWF with subnanomolar affinity at a well-defined epitope in the C-terminal cysteine-knot (CK) domain, which is spatially distant from regions mediating VWF's hemostatic functions. Consistent with structural analyses, in vitro functional studies demonstrated that HMB-002-bound VWF retained its ability to bind factor VIII (FVIII), platelet GPIbα, and collagen, as well as susceptibility to proteolytic regulation by ADAMTS13. In cynomolgus monkeys, IV and subcutaneous administration of HMB-002 resulted in time-dependent accumulation of endogenous VWF and FVIII antigen, reaching about twofold elevation with a proportional increase in VWF activity and with retained VWF multimer distribution. HMB-002 also extended the half-life of coadministered recombinant VWF by approximately threefold. Using a surrogate antibody with overlapping epitope specificity, similar VWF accumulation was observed in a type 1 VWD mouse model with improved hemostasis following vascular challenge. By elevating levels of circulating VWF and FVIII, HMB-002 represents a potential subcutaneous prophylactic treatment approach to mitigate the hemostatic impairment in VWD and address current limitations in disease management.


  • Organizational Affiliation
    • Hemab Therapeutics, Copenhagen, Denmark.

Macromolecule Content 

  • Total Structure Weight: 61.25 kDa 
  • Atom Count: 4,150 
  • Modeled Residue Count: 528 
  • Deposited Residue Count: 550 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
von Willebrand factorA [auth D]113Macaca fascicularisMutation(s): 0 
Gene Names: VWF
UniProt
Find proteins for A0A2K5X4G5 (Macaca fascicularis)
Explore A0A2K5X4G5 
Go to UniProtKB:  A0A2K5X4G5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K5X4G5
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
VH-CH1B [auth H]224synthetic constructMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Kappa light chainC [auth L]213synthetic constructMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth D]
G [auth H]
H
I [auth H]
J [auth L]
E [auth D],
G [auth H],
H,
I [auth H],
J [auth L],
K [auth L],
L,
M [auth L],
N [auth L],
O [auth L],
P [auth L],
Q [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth H]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
R [auth L]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.249 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.976α = 90
b = 116.327β = 90
c = 252.463γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-11
    Type: Initial release
  • Version 1.1: 2026-08-26
    Changes: Database references