5TH9

Structure determination of a potent, selective antibody inhibitor of human MMP9 (GS-5745 bound to MMP-9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.999 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biochemical characterization and structure determination of a potent, selective antibody inhibitor of human MMP9.

Appleby, T.C.Greenstein, A.E.Hung, M.Liclican, A.Velasquez, M.Villasenor, A.G.Wang, R.Wong, M.H.Liu, X.Papalia, G.A.Schultz, B.E.Sakowicz, R.Smith, V.Kwon, H.J.

(2017) J. Biol. Chem. 292: 6810-6820

  • DOI: 10.1074/jbc.M116.760579
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Matrix metalloproteinase 9 (MMP9) is a member of a large family of proteases that are secreted as inactive zymogens. It is a key regulator of the extracellular matrix, involved in the degradation of various extracellular matrix proteins. MMP9 plays a ...

    Matrix metalloproteinase 9 (MMP9) is a member of a large family of proteases that are secreted as inactive zymogens. It is a key regulator of the extracellular matrix, involved in the degradation of various extracellular matrix proteins. MMP9 plays a pathological role in a variety of inflammatory and oncology disorders and has long been considered an attractive therapeutic target. GS-5745, a potent, highly selective humanized monoclonal antibody inhibitor of MMP9, has shown promise in treating ulcerative colitis and gastric cancer. Here we describe the crystal structure of GS-5745·MMP9 complex and biochemical studies to elucidate the mechanism of inhibition of MMP9 by GS-5745. GS-5745 binds MMP9 distal to the active site, near the junction between the prodomain and catalytic domain, and inhibits MMP9 by two mechanisms. Binding to pro-MMP9 prevents MMP9 activation, whereas binding to active MMP9 allosterically inhibits activity.


    Organizational Affiliation

    From Gilead Sciences, Inc., Foster City, California 94404.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GS-5745 Fab light chain
L, M, N
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GS-5745 Fab heavy chain
H, I, J
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Matrix metalloproteinase-9,Matrix metalloproteinase-9
A, B, C
231Homo sapiensMutation(s): 0 
Gene Names: MMP9 (CLG4B)
EC: 3.4.24.35
Find proteins for P14780 (Homo sapiens)
Go to Gene View: MMP9
Go to UniProtKB:  P14780
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NCO
Query on NCO

Download SDF File 
Download CCD File 
A, B, C
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.999 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 168.167α = 90.00
b = 168.167β = 90.00
c = 234.735γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references