Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 39044.85 
• Atom Count: 2796 
• 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): 1 


• 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 

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:  
  4I03, 4H84, 4H82, 4H76, 4H49, 4H3X, 4H30, 4H2E, 4H1Q
• Also Cited By: 4H84, 4H76, 4H3X


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Matrix metalloproteinase-9	A, B	160	Homo sapiens	Mutation(s): 1  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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MLT	B	D-MALATE (2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
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
PEG	A, B	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PGO	A, B	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 73.870	α = 90.00
b = 98.240	β = 90.00
c = 47.440	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
DNA	data collection
REFMAC	refinement
MOLREP	phasing
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
  Type: Database references
• Version 1.2: 2014-10-08
  Type: Structure summary
• Version 1.3: 2015-08-12
  Type: Database references
• Version 1.4: 2017-08-09
  Type: Data collection, Refinement description, Source and taxonomy