3O2X: MMP-13

MMP-13 in complex with selective tetrazole core inhibitor. Determined by X-ray diffraction at 1.9 Å resolution. Released 10 Aug 2011.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,167
Mol. weight: 78.37 kDa
Ligands: 3O2, ZN, CA
Released: 10 Aug 2011

Explore 3O2X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3O2X contains 15 α-helices and 32 β-strands across 4 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: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1117-1122	6	1
β-strand	1125	1	2
α-helix	1131-1146	16
β-strand	1152-1156	5	1
β-strand	1163-1168	6	1
β-strand	1186-1188	3	1
β-strand	1199-1202	4	1
β-strand	1207-1208	2	3
β-strand	1214-1215	2	3
α-helix	1216-1227	12
α-helix	1256-1266	11

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2106-2108	3
β-strand	2117-2122	6	4
β-strand	2125	1	5
α-helix	2131-2146	16
β-strand	2152-2156	5	4
β-strand	2163-2168	6	4
β-strand	2186-2188	3	4
β-strand	2199-2202	4	4
β-strand	2207-2208	2	6
β-strand	2214-2215	2	6
α-helix	2216-2228	13
α-helix	2256-2266	11

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1117-1122	6	7
β-strand	1125	1	2
α-helix	1131-1146	16
β-strand	1152-1155	4	7
β-strand	1163-1168	6	7
β-strand	1186-1188	3	7
α-helix	1189-1190	2
β-strand	1199-1202	4	7
β-strand	1207-1208	2	8
β-strand	1214-1215	2	8
α-helix	1216-1228	13
α-helix	1256-1266	11

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2117-2122	6	9
β-strand	2125	1	5
α-helix	2131-2146	16
β-strand	2152-2156	5	9
β-strand	2163-2168	6	9
β-strand	2186-2188	3	9
α-helix	2189-2190	2
β-strand	2199-2202	4	9
β-strand	2207-2208	2	10
β-strand	2214-2215	2	10
α-helix	2216-2228	13
α-helix	2256-2266	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Collagenase 3	A, B, C, D	protein	164	Homo sapiens	P45452 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3O2X_1 Collagenase 3 (chains A, B, C, D)
ANVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADI
MISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHE
FGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYG

Ligands and cofactors

ID	Name	Formula	Copies
3O2	N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetraz…	C26 H31 F3 N6 O7 S	4
ZN	Zinc ion	Zn	8
CA	Calcium ion	Ca	8

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

Primary citation

MMP-13 in complex with selective tetrazole core inhibitor. Barta, T.E., Becker, D.P., Bedell, L.J. et al. To be published.

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

Browse structure collections

About this viewer

MolViewer shows 3O2X directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.