7U5B

Structure of Human KLK5 bound to anti-KLK5 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dual antibody inhibition of KLK5 and KLK7 for Netherton syndrome and atopic dermatitis.

Chavarria-Smith, J.Chiu, C.P.C.Jackman, J.K.Yin, J.Zhang, J.Hackney, J.A.Lin, W.Y.Tyagi, T.Sun, Y.Tao, J.Dunlap, D.Morton, W.D.Ghodge, S.V.Maun, H.R.Li, H.Hernandez-Barry, H.Loyet, K.M.Chen, E.Liu, J.Tam, C.Yaspan, B.L.Cai, H.Balazs, M.Arron, J.R.Li, J.Wittwer, A.J.Pappu, R.Austin, C.D.Lee, W.P.Lazarus, R.A.Sudhamsu, J.Koerber, J.T.Yi, T.

(2022) Sci Transl Med 14: eabp9159-eabp9159

  • DOI: https://doi.org/10.1126/scitranslmed.abp9159
  • Primary Citation of Related Structures:  
    7U5B

  • PubMed Abstract: 

    The epidermis is a barrier that prevents water loss while keeping harmful substances from penetrating the host. The impermeable cornified layer of the stratum corneum is maintained by balancing continuous turnover driven by epidermal basal cell proliferation, suprabasal cell differentiation, and corneal shedding. The epidermal desquamation process is tightly regulated by balance of the activities of serine proteases of the Kallikrein-related peptidases (KLK) family and their cognate inhibitor lymphoepithelial Kazal type-related inhibitor (LEKTI), which is encoded by the serine peptidase inhibitor Kazal type 5 gene. Imbalance of proteolytic activity caused by a deficiency of LEKTI leads to excessive desquamation due to increased activities of KLK5, KLK7, and KLK14 and results in Netherton syndrome (NS), a debilitating condition with an unmet clinical need. Increased activity of KLKs may also be pathological in other dermatoses such as atopic dermatitis (AD). Here, we describe the discovery of inhibitory antibodies against murine KLK5 and KLK7 that could compensate for the deficiency of LEKTI in NS. These antibodies are protective in mouse models of NS and AD and, when combined, promote improved skin barrier integrity and reduced inflammation. To translate these findings, we engineered a humanized bispecific antibody capable of potent inhibition of human KLK5 and KLK7. A crystal structure of KLK5 bound to the inhibitory Fab revealed that the antibody binds distal to its active site and uses a relatively unappreciated allosteric inhibition mechanism. Treatment with the bispecific anti-KLK5/7 antibody represents a promising therapy for clinical development in NS and other inflammatory dermatoses.


  • Organizational Affiliation

    Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-KLK5 Fab Heavy ChainA,
C [auth H]
224synthetic constructMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-KLK5 Fab Light ChainB,
E [auth L]
217synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Kallikrein-5D [auth J],
F [auth I]
227Homo sapiensMutation(s): 0 
Gene Names: KLK5SCTEUNQ570/PRO1132
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y337 (Homo sapiens)
Explore Q9Y337 
Go to UniProtKB:  Q9Y337
PHAROS:  Q9Y337
GTEx:  ENSG00000167754 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y337
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth H],
M [auth H],
N [auth H],
O [auth J],
P [auth J],
Q [auth L],
R [auth L],
S [auth L],
T [auth I],
U [auth I]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.686α = 90
b = 283.624β = 90
c = 295.575γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
F. Hoffmann-La Roche LTDSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description