5UWK: Matrix metalloproteinase-13

Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-10a. Determined by X-ray diffraction at 1.6 Å resolution. Released 12 Jul 2017.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,000
Mol. weight: 40.26 kDa
Ligands: 8OM, CA, ZN
Released: 12 Jul 2017

Explore 5UWK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UWK contains 10 α-helices and 14 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, 7 β-strands

Element	Residues	Length	Sheet
β-strand	117-122	6	1
α-helix	131-146	16
β-strand	152-155	4	1
β-strand	163-168	6	1
β-strand	186-188	3	1
α-helix	189-190	2
β-strand	199-202	4	1
α-helix	206	1
β-strand	207-208	2	2
β-strand	214-215	2	2
α-helix	216-227	12
α-helix	256-266	11

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	117-122	6	3
α-helix	131-146	16
β-strand	152-155	4	3
β-strand	163-168	6	3
β-strand	186-188	3	3
α-helix	189-190	2
β-strand	199-202	4	3
α-helix	206	1
β-strand	207-208	2	4
β-strand	214-215	2	4
α-helix	216-228	13
α-helix	256-266	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Collagenase 3	A, B	protein	172	Homo sapiens	P45452 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5UWK_1 Collagenase 3 (chains A, B)
MYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIAD
IMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAH
EFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN

Ligands and cofactors

ID	Name	Formula	Copies
8OM	(S)-3-methyl-2-(4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)t…	C25 H27 N3 O5 S2	2
CA	Calcium ion	Ca	6
ZN	Zinc ion	Zn	4

Primary citation

Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. Choi, J.Y., Fuerst, R., Knapinska, A.M. et al. J Med Chem (2017) 60:5816-5825. DOI 10.1021/acs.jmedchem.7b00514 · 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…
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
2OW9 1.74 Å, Crystal structure analysis of the MMP13 catalytic domain in complex with specific…

Browse structure collections

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