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: 19.84 kDa 
• Atom Count: 1393 
• Modelled Residue Count: 171 
• Deposited Residue Count: 171 
• Unique protein chains: 1

1EUB

SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED TO A POTENT NON-PEPTIDIC SULFONAMIDE INHIBITOR

• PDB DOI: 10.2210/pdb1EUB/pdb

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


• Deposited: 2000-04-14 Released: 2001-04-14 
• Deposition Author(s): Zhang, X., Gonnella, N.C., Koehn, J., Pathak, N., Ganu, V., Melton, R., Parker, D., Hu, S.I., Nam, K.Y.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,TARGET FUNCTION 

Literature

Solution structure of the catalytic domain of human collagenase-3 (MMP-13) complexed to a potent non-peptidic sulfonamide inhibitor: binding comparison with stromelysin-1 and collagenase-1.

Zhang, X., Gonnella, N.C., Koehn, J., Pathak, N., Ganu, V., Melton, R., Parker, D., Hu, S.I., Nam, K.Y.

(2000) J Mol Biol 301: 513-524

• PubMed: 10926524 
• DOI: 10.1006/jmbi.2000.3988
• Primary Citation of Related Structures:  
  1EUB


• PubMed Abstract: 
  

The full three-dimensional structure of the catalytic domain of human collagenase-3 (MMP-13) complexed to a potent, sulfonamide hydroxamic acid inhibitor (CGS 27023) has been determined by NMR spectroscopy. The results reveal a core domain for the protein consisting of three alpha-helices and five beta-sheet strands with an overall tertiary fold similar to the catalytic domains of other matrix metalloproteinase family members. The S1' pocket, which is the major site of hydrophobic binding interaction, was found to be a wide cleft spanning the length of the protein and presenting facile opportunity for inhibitor extension deep into the pocket. Comparison with the reported X-ray structure of collagenase-3 showed evidence of flexibility for the loop region flanking the S1' pocket in both NMR and X-ray data. This flexibility was corroborated by NMR dynamics studies. Inhibitor binding placed the methoxy phenyl ring in the S1' pocket with the remainder of the molecule primarily solvent-exposed. The binding mode for this inhibitor was found to be similar with respect to stromelysin-1 and collagenase-1; however, subtle comparative differences in the interactions between inhibitor and enzyme were observed for the three MMPs that were consistent with their respective binding potencies.

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Organizational Affiliation: 

Novartis Institute for Biomedical Research, 556 Morris Ave., Summit, NJ 07901, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COLLAGENASE 3	A	171	Homo sapiens	Mutation(s): 0  Gene Names: MMP13 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens) Explore P45452  Go to UniProtKB:  P45452
PHAROS:  P45452

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MSB	H [auth A]	1-METHYLOXY-4-SULFONE-BENZENE C7 H8 O3 S XUNSZADDFLWFOL-UHFFFAOYSA-N
HAV	F [auth A]	HYDROXYAMINOVALINE C5 H12 N2 O2 USSBBYRBOWZYSB-SCSAIBSYSA-N
3MP	G [auth A]	3-METHYLPYRIDINE C6 H7 N ITQTTZVARXURQS-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,TARGET FUNCTION 
• OLDERADO: 1EUB Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-04-14 
• Released Date: 2001-04-14 
Deposition Author(s): Zhang, X., Gonnella, N.C., Koehn, J., Pathak, N., Ganu, V., Melton, R., Parker, D., Hu, S.I., Nam, K.Y.

Revision History  

• Version 1.0: 2001-04-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Data collection, Database references, Derived calculations