3KRY: MMP-13

Crystal structure of MMP-13 in complex with SC-78080. Determined by X-ray diffraction at 1.9 Å resolution. Released 6 Oct 2010.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,886
Mol. weight: 76.95 kDa
Ligands: ZN, 3KR, CA
Released: 6 Oct 2010

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

Secondary structure: helices and β-sheets

3KRY contains 18 α-helices and 34 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: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	106-108	3
β-strand	110	1	1
β-strand	117-122	6	2
α-helix	131-146	16
β-strand	152-156	5	2
β-strand	163-168	6	2
β-strand	186-188	3	2
α-helix	189-190	2
β-strand	199-202	4	2
β-strand	207-208	2	3
β-strand	214-215	2	3
α-helix	216-228	13
β-strand	230-231	2	4
α-helix	256-266	11

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	106-108	3
β-strand	117-122	6	5
β-strand	125	1	6
α-helix	131-146	16
β-strand	152-156	5	5
β-strand	163-168	6	5
β-strand	186-188	3	5
β-strand	199-202	4	5
β-strand	207-208	2	7
β-strand	214-215	2	7
α-helix	216-228	13
α-helix	256-266	11

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	107-109	3
β-strand	117-122	6	8
α-helix	131-146	16
β-strand	152-155	4	8
β-strand	163-168	6	8
β-strand	186-188	3	8
α-helix	189-190	2
β-strand	199-202	4	8
β-strand	207-208	2	9
β-strand	214-215	2	9
α-helix	216-228	13
α-helix	256-266	11

Chain D: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	105-106	2	4
β-strand	108	1	1
β-strand	117-122	6	10
β-strand	125	1	6
α-helix	131-146	16
β-strand	152-155	4	10
β-strand	163-168	6	10
β-strand	186-188	3	10
α-helix	189-190	2
β-strand	199-202	4	10
β-strand	207-208	2	11
β-strand	214-215	2	11
α-helix	216-228	13
α-helix	256-266	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

>3KRY_1 Collagenase 3 (chains A, B, C, D)
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADI
MISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHE
FGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
3KR	1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)pip…	C22 H23 F3 N2 O7 S	4
CA	Calcium ion	Ca	8

Primary citation

Orally-active MMP-1 sparing alpha-tetrahydropyranyl and alpha-piperidinyl sulfone matrix metalloproteinase (MMP) inhibitors with efficacy in cancer, arthritis, and cardiovascular disease. Becker, D.P., Barta, T.E., Bedell, L.J. et al. J Med Chem (2010) 53:6653-6680. DOI 10.1021/jm100669j · 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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