4JA1

Structure of MMP3 complexed with a platinum-based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4JA1/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-18 Released: 2013-02-27 
• Deposition Author(s): Belviso, B.D., Arnesano, F., Calderone, V., Caliandro, R., Natile, G., Siliqi, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.244 
• R-Value Work: 0.195 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Structure of matrix metalloproteinase-3 with a platinum-based inhibitor.

Belviso, B.D., Caliandro, R., Siliqi, D., Calderone, V., Arnesano, F., Natile, G.

(2013) Chem Commun (Camb) 49: 5492-5494

• PubMed: 23660647 
• DOI: https://doi.org/10.1039/c3cc41278d
• Primary Citation of Related Structures:  
  4DPE, 4G9L, 4JA1


• PubMed Abstract: 
  

  An X-ray investigation has been performed with the aim of characterizing the binding sites of a platinum-based inhibitor (K[PtCl3(DMSO)]) of matrix metalloproteinase-3 (stromelysin-1). The platinum complex targets His224 in the S1' specificity loop, representing the first step in the selective inhibition process (PDB ID code 4JA1).

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Organizational Affiliation: 

Institute of Crystallography, Consiglio Nazionale delle Ricerche, via Amendola 122/o, 70126 Bari, Italy.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 40.38 kDa 
• Atom Count: 2,809 
• Modelled Residue Count: 335 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromelysin-1	A, B	173	Homo sapiens	Mutation(s): 0  Gene Names: MMP3, STMY1 EC: 3.4.24.17
UniProt & NIH Common Fund Data Resources
Find proteins for P08254 (Homo sapiens) Explore P08254  Go to UniProtKB:  P08254
PHAROS:  P08254 GTEx:  ENSG00000149968

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGH	O [auth B]	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID C13 H20 N2 O5 S JIRXORZYIXSWOB-UHFFFAOYSA-N
PT	H [auth A], P [auth B], Q [auth B]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	I [auth A], R [auth B], S [auth B], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
NGH	BindingDB:  4JA1	Ki: min: 132, max: 133 (nM) from 2 assay(s)
		IC50: 6500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.244 
• R-Value Work: 0.195 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.119	α = 90
b = 77.615	β = 90
c = 106.048	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
ILMILIONE	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
ILMILIONE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Belviso, B.D., Arnesano, F., Calderone, V., Caliandro, R., Natile, G., Siliqi, D.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2013-05-15
  Changes: Database references
• Version 1.2: 2013-05-22
  Changes: Database references
• Version 1.3: 2013-05-29
  Changes: Structure summary
• Version 1.4: 2013-06-05
  Changes: Database references
• Version 1.5: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description