Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 38.89 kDa 
• Atom Count: 2771 
• Residue Count: 332 
• Unique protein chains: 1

2D1N

Collagenase-3 (MMP-13) complexed to a hydroxamic acid inhibitor

• DOI: 10.2210/pdb2D1N/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-08-29 Released: 2006-06-27 
• Deposition Author(s): Kohno, T., Hochigai, H., Yamashita, E., Tsukihara, T., Kanaoka, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.239 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453

Kohno, T., Hochigai, H., Yamashita, E., Tsukihara, T., Kanaoka, M.

(2006) Biochem Biophys Res Commun 344: 315-322

• PubMed: 16603129 
• DOI: 10.1016/j.bbrc.2006.03.098
• Primary Citation of Related Structures:  
  2D1N, 2D1O


• PubMed Abstract: 
  

Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453 have been solved at 2.01 and 2.37A resolutions, respectively. The results revealed that the binding modes for this inhibitor to MMP-3 and -13 were quite similar. However, subtle comparative differences were observed at the bottom of S1' pockets, which were occupied with the guanidinomethyl moiety of the inhibitor. A remarkable feature of the inhibitor was the deep penetration of its long aliphatic chain into the S1' pocket and exposure of the guanidinomethyl moiety to the solvent.

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Organizational Affiliation: 

Drug Research Division, Dainippon Sumitomo Pharma Co., Ltd., 3-1-98 Kasugadenaka, Konohana-ku, Osaka 554-0022, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagenase 3	A, B	166	Homo sapiens	Mutation(s): 0  Gene Names: MMP13 EC: 3.4.24
Find proteins for P45452 (Homo sapiens) Explore P45452  Go to UniProtKB:  P45452
NIH Common Fund Data Resources
PHAROS:  P45452 GTEx:  ENSG00000137745

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FA4	A, B	SM-25453 C24 H42 N6 O3 DPKFTMHWVJEOMW-OAQYLSRUSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
FA4	Ki :  7   nM  PDBBind
FA4	Ki:  7   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.239 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.47	α = 90
b = 96.47	β = 90
c = 67.52	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-29 
• Released Date: 2006-06-27 
Deposition Author(s): Kohno, T., Hochigai, H., Yamashita, E., Tsukihara, T., Kanaoka, M.

Revision History 

• Version 1.0: 2006-06-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-07-18
  Changes: Data collection