Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.18 kDa 
• Atom Count: 1271 
• Modelled Residue Count: 159 
• Deposited Residue Count: 159 
• Unique protein chains: 1

1Z3J

Solution Structure of MMP12 in the presence of N-isobutyl-N-4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH)

• PDB DOI: 10.2210/pdb1Z3J/pdb
• BMRB: 6444

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


• Deposited: 2005-03-13 Released: 2005-04-19 
• Deposition Author(s): Bertini, I., Calderone, V., Cosenza, M., Fragai, M., Lee, Y.M., Luchinat, C., Mangani, S., Terni, B., Turano, P.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 1 
• Selection Criteria: minimized average structure 

Literature

Conformational variability of matrix metalloproteinases: Beyond a single 3D structure.

Bertini, I., Calderone, V., Cosenza, M., Fragai, M., Lee, Y.M., Luchinat, C., Mangani, S., Terni, B., Turano, P.

(2005) Proc Natl Acad Sci U S A 102: 5334-5339

• PubMed: 15809432 
• DOI: 10.1073/pnas.0407106102
• Primary Citation of Related Structures:  
  1RMZ, 1Y93, 1YCM, 1Z3J


• PubMed Abstract: 
  

The structures of the catalytic domain of matrix metalloproteinase 12 in the presence of acetohydroxamic acid and N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid have been solved by x-ray diffraction in the crystalline state at 1.0 and 1.3-A resolution, respectively, and compared with the previously published x-ray structure at 1.2-A resolution of the adduct with batimastat. The structure of the N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid adduct has been solved by NMR in solution. The three x-ray structures and the solution structure are similar but not identical to one another, the differences being sizably higher in the loops. We propose that many of the loops show a dynamical behavior in solution on a variety of time scales. Different conformations of some flexible regions of the protein can be observed as "frozen" in different crystalline environments. The mobility in solution studied by NMR reveals conformational equilibria in accessible time scales, i.e., from 10(-5) s to ms and more. Averaging of some residual dipolar couplings is consistent with further motions down to 10(-9) s. Finally, local thermal motions of each frozen conformation in the crystalline state at 100 K correlate well with local motions on the picosecond time scale. Flexibility/conformational heterogeneity in crucial parts of the catalytic domain is a rule rather than an exception in matrix metalloproteinases, and its extent may be underestimated by inspection of one x-ray structure. Backbone flexibility may play a role in the difficulties encountered in the design of selective inhibitors, whereas it may be a requisite for substrate binding and broad substrate specificity.

---

Organizational Affiliation: 

Magnetic Resonance Center (Centro di Risonanze Magnetiche), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	159	Homo sapiens	Mutation(s): 1  Gene Names: MMP12, HME 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
NGH	G [auth A]	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID C13 H20 N2 O5 S JIRXORZYIXSWOB-UHFFFAOYSA-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
NGH	BindingDB:  1Z3J	Ki: 4.3 (nM) from 1 assay(s)
	PDBBind:  1Z3J	Kd: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 1 
• Selection Criteria: minimized average structure 
• OLDERADO: 1Z3J Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-13 
• Released Date: 2005-04-19 
Deposition Author(s): Bertini, I., Calderone, V., Cosenza, M., Fragai, M., Lee, Y.M., Luchinat, C., Mangani, S., Terni, B., Turano, P.

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Data collection, Database references, Derived calculations