2OW9: Collagenase 3

Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor. Determined by X-ray diffraction at 1.74 Å resolution. Released 27 Feb 2007.

Method: X-ray diffraction
Resolution: 1.74 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,195
Mol. weight: 39.71 kDa
Ligands: HAE, SP6, CA, ZN
Released: 27 Feb 2007

Explore 2OW9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OW9 contains 10 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	84-85	2	1
α-helix	86-87	2
β-strand	96-101	6	2
α-helix	110-125	16
β-strand	131-135	5	2
β-strand	142-147	6	2
β-strand	165-167	3	2
α-helix	168-169	2
β-strand	178-181	4	2
β-strand	186-187	2	3
β-strand	193-194	2	3
α-helix	195-207	13
β-strand	209-210	2	4
α-helix	235-245	11

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	84-85	2	4
α-helix	86-88	3
β-strand	96-101	6	5
α-helix	110-125	16
β-strand	131-134	4	5
β-strand	142-147	6	5
β-strand	165-167	3	5
α-helix	168-169	2
β-strand	178-181	4	5
β-strand	186-187	2	6
β-strand	193-194	2	6
α-helix	195-206	12
β-strand	209-210	2	1
α-helix	235-245	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Collagenase 3	A, B	protein	170	Homo sapiens	P45452 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2OW9_1 Collagenase 3 (chains A, B)
MASYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGI
ADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVA
AHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGD

Ligands and cofactors

ID	Name	Formula	Copies
HAE	Acetohydroxamic acid	C2 H5 N O2	2
SP6	Benzyl 6-benzyl-5,7-dioxo-6,7-dihydro-5H-[1,3]THIAZOLO[3,2-c]pyrimidine-2-carbo…	C21 H16 N2 O4 S	2
CA	Calcium ion	Ca	7
ZN	Zinc ion	Zn	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia side effects. Johnson, A.R., Pavlovsky, A.G., Ortwine, D.F. et al. J Biol Chem (2007) 282:27781-27791. DOI 10.1074/jbc.M703286200 · PubMed

Other PDB entries of the same protein (UniProt P45452 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5B5O 1.2 Å, Crystal structure of the catalytic domain of MMP-13 complexed with…
3ZXH 1.3 Å, MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor
4JP4 1.43 Å, Mmp13 in complex with a reverse hydroxamate Zn-binder
3WV3 1.6 Å, Crystal structure of the catalytic domain of MMP-13 complexed with…
5B5P 1.6 Å, Crystal structure of the catalytic domain of MMP-13 complexed with…
5UWK 1.6 Å, Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-10a
830C 1.6 Å, Collagenase-3 (mmp-13) complexed to a sulphone-based hydroxamic acid
5UWM 1.62 Å, Matrix metalloproteinase-13 complexed with selective inhibitor compound (R)-17a
4L19 1.66 Å, Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1
1XUC 1.7 Å, Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor
2YIG 1.7 Å, MMP13 in complex with a novel selective non zinc binding inhibitor
6HV2 1.71 Å, MMP-13 in complex with the peptide IMISF

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