ISDA: 2D1N

Deposition Date 2005-08-29

Release Date 2006-06-27

Last Version Date 2023-10-25

Entry Detail

PDB ID:

2D1N

Keywords:

HYDROLASE

Title:

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

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.37 Å

R-Value Free:

0.23

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 32

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Collagenase 3
Gene (Uniprot):MMP13
Chain IDs:A, B
Chain Length:166
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P45452 Pfam ID:PF00413 EC:3.4.24.17

Ligand Molecules

FA4

Primary Citation

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.Show

Biochem.Biophys.Res.Commun. 344 315 322 (2006)

PMID: 16603129 DOI: 10.1016/j.bbrc.2006.03.098

Abstact

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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Primary Citation of related structures

Abstact

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