5UWM: Matrix metalloproteinase-13

Matrix metalloproteinase-13 complexed with selective inhibitor compound (R)-17a. Determined by X-ray diffraction at 1.62 Å resolution. Released 12 Jul 2017.

Method: X-ray diffraction
Resolution: 1.62 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,011
Mol. weight: 41.28 kDa
Ligands: 8OA, CA, ZN
Released: 12 Jul 2017

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

Secondary structure: helices and β-sheets

5UWM contains 9 α-helices and 16 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	117-122	6	1
α-helix	131-146	16
β-strand	152-156	5	1
β-strand	163-168	6	1
β-strand	186-188	3	1
α-helix	189-190	2
β-strand	199-202	4	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: 4 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
β-strand	207-208	2	4
β-strand	214-215	2	4
α-helix	216-227	12
α-helix	256-266	11

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	212-213	2
β-strand	214	1	1

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	214	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Collagenase 3	A, B	protein	172	Homo sapiens	P45452 (AlphaFold model)
Collagenase 3	C, D	protein	5	Homo sapiens	P45452 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5UWM_1 Collagenase 3 (chains A, B)
MYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIAD
IMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAH
EFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN

Sequence of entity 2 (C, D), FASTA

>5UWM_2 Collagenase 3 (chains C, D)
VTPLN

Ligands and cofactors

ID	Name	Formula	Copies
8OA	(R)-N-(3-methyl-1-(methylamino)-1-oxobutan-2-yl)-5-(4-(((4-oxo-4,5,6,7-tetrahyd…	C25 H28 N4 O4 S	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…
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
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…

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