Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.04 kDa 
• Atom Count: 3141 
• Residue Count: 320 
• Unique protein chains: 1

4HMA

Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the MMP-9 catalytic domain

• DOI: 10.2210/pdb4HMA/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-10-18 Released: 2013-04-24 
• Deposition Author(s): Stura, E.A., Antoni, C., Vera, L., Nuti, E., Carafa, L., Cassar-Lajeunesse, E., Dive, V., Rossello, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.283 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Literature

Crystallization of bi-functional ligand protein complexes.

Antoni, C., Vera, L., Devel, L., Catalani, M.P., Czarny, B., Cassar-Lajeunesse, E., Nuti, E., Rossello, A., Dive, V., Stura, E.A.

(2013) J Struct Biol 182: 246-254

• PubMed: 23567804 
• DOI: 10.1016/j.jsb.2013.03.015
• Primary Citation of Related Structures:  
  4H3X, 4H49, 4H76, 4H84, 4H82, 4H1Q, 4H30, 4H2E, 4HMA, 4I03


• PubMed Abstract: 
  

Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects.

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Related Citations: 

• A new development of matrix metalloproteinase inhibitors: twin hydroxamic acids as potent inhibitors of MMPs.
  Rossello, A., Nuti, E., Catalani, M.P., Carelli, P., Orlandini, E., Rapposelli, S., Tuccinardi, T., Atkinson, S.J., Murphy, G., Balsamo, A.
  (2005) Bioorg Med Chem Lett 15: 2311

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Organizational Affiliation: 

CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines-SIMOPRO, Gif-sur-Yvette F-91191, France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix metalloproteinase-9	A, B	160	Homo sapiens	Mutation(s): 1  Gene Names: CLG4B, MMP9 EC: 3.4.24.35
Find proteins for P14780 (Homo sapiens) Explore P14780  Go to UniProtKB:  P14780
NIH Common Fund Data Resources
PHAROS:  P14780 GTEx:  ENSG00000100985

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0ZD	A	N,N'-bis(2-[(biphenyl-4ylsulfonyl)[(2R)-1-hydroxy-3-methyl-1-oxobutan-2-yl]-amino]ethyl)benzene-1,3-dicarboxamide C46 H50 N4 O10 S2 JEFGHXXQQOIPKU-NCRNUEESSA-N
MLT	B	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
PEG	A, B	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PGO	A, B	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0ZD	IC50:  26   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.283 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.87	α = 90
b = 98.24	β = 90
c = 47.44	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-18 
• Released Date: 2013-04-24 
Deposition Author(s): Stura, E.A., Antoni, C., Vera, L., Nuti, E., Carafa, L., Cassar-Lajeunesse, E., Dive, V., Rossello, A.

Revision History 

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2013-05-01
  Changes: Database references
• Version 1.2: 2014-10-08
  Changes: Structure summary
• Version 1.3: 2015-08-12
  Changes: Database references
• Version 1.4: 2017-08-09
  Changes: Data collection, Refinement description, Source and taxonomy