4H82

Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb4H82/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-09-21 Released: 2013-05-01 
• Deposition Author(s): Antoni, C., Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Dive, V., Rossello, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Starting Model: experimental

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: https://doi.org/10.1016/j.jsb.2013.03.015
• Primary Citation of Related Structures:  
  4H1Q, 4H2E, 4H30, 4H3X, 4H49, 4H76, 4H82, 4H84, 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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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.7 kDa 
• Atom Count: 6,145 
• Modelled Residue Count: 640 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L29	EA [auth D], J [auth A]	N,N'-bis(2-{(biphenyl-4-ylsulfonyl)[(2R)-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]amino}ethyl)benzene-1,3-dicarboxamide (non-preferred name) C46 H52 N6 O10 S2 JPMXJRBHCOULJI-NCRNUEESSA-N
PEG	BA [auth C], KA [auth D], U [auth C], V [auth C], X [auth C], Y [auth C], Z [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	AA [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PGO	CA [auth D], JA [auth D], LA [auth D]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
PPI	W [auth C]	PROPANOIC ACID C3 H6 O2 XBDQKXXYIPTUBI-UHFFFAOYSA-N
ZN	DA [auth D], E [auth A], F [auth A], FA [auth D], K [auth B], L [auth B], P [auth C], Q [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
L29	BindingDB:  4H82	IC50: 5.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.9	α = 90.03
b = 98.86	β = 111.95
c = 47.13	γ = 89.98

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Antoni, C., Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Dive, V., Rossello, A.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2014-10-08
  Changes: Database references
• Version 1.2: 2014-10-15
  Changes: Derived calculations
• Version 1.3: 2015-08-12
  Changes: Database references
• Version 1.4: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.5: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description