3EHY

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor (R)-2-(4-methoxyphenylsulfonamido)propanoic acid

• PDB DOI: https://doi.org/10.2210/pdb3EHY/pdb

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


• Deposited: 2008-09-15 Released: 2009-05-19 
• Deposition Author(s): Calderone, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.155 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Biotin-tagged probes for MMP expression and activation: design, synthesis, and binding properties

Dragoni, E., Calderone, V., Fragai, M., Jaiswal, R., Luchinat, C., Nativi, C.

(2009) Bioconjug Chem 20: 719-727

• PubMed: 19275207 
• DOI: https://doi.org/10.1021/bc8003827
• Primary Citation of Related Structures:  
  3EHX, 3EHY


• PubMed Abstract: 
  

  The design and synthesis of biotin chain-terminated inhibitors (BTI) showing high affinity for matrix metalloproteinases (MMPs) on one side and high affinity for avidin through the biotinylated tag on the other are reported. The affinity of the designed BTI toward five different MMPs has been evaluated and the simultaneous formation of a highly stable ternary system Avidin-BTI-MMP clearly assessed. This system will permit the development of new approaches to detect, quantify, or collect MMPs in biological samples, with potential applications in vivo.

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Organizational Affiliation: 

Magnetic Resonance Center - University of Florence, Sesto Fiorentino, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 17.99 kDa 
• Atom Count: 1,396 
• Modelled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	158	Homo sapiens	Mutation(s): 1  Gene Names: MMP12 EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens) Explore P39900  Go to UniProtKB:  P39900
PHAROS:  P39900 GTEx:  ENSG00000262406

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBL	G [auth A]	N-[(4-methoxyphenyl)sulfonyl]-D-alanine C10 H13 N O5 S XTCIPBHRVYICGT-SSDOTTSWSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TBL	PDBBind:  3EHY	Ki: 1400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.155 
• R-Value Observed: 0.159 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.256	α = 90
b = 60.479	β = 116.17
c = 54.598	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Calderone, V.

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description