5B5O: Catalytic domain of MMP-13

Crystal structure of the catalytic domain of MMP-13 complexed with N-phenyl-4-((4H-1,2,4-triazol-3-ylsulfanyl)methyl)-1,3-thiazol-2-amine. Determined by X-ray diffraction at 1.2 Å resolution. Released 18 Jan 2017.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,299
Mol. weight: 39.84 kDa
Ligands: WMM, CA, ZN
Released: 18 Jan 2017

Explore 5B5O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B5O contains 9 α-helices and 20 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	106	1	1
α-helix	107-108	2
β-strand	110	1	2
β-strand	117-122	6	3
α-helix	131-146	16
β-strand	152-156	5	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	216-228	13
β-strand	230	1	5
α-helix	256-266	11

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	106	1	5
β-strand	108	1	2
β-strand	117-122	6	6
α-helix	131-146	16
β-strand	152-155	4	6
β-strand	163-168	6	6
β-strand	186-188	3	6
α-helix	189-190	2
β-strand	199-202	4	6
β-strand	207-208	2	7
β-strand	214-215	2	7
α-helix	216-228	13
β-strand	230	1	1
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

>5B5O_1 Collagenase 3 (chains A, B)
EYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIAD
IMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAH
EFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN

Ligands and cofactors

ID	Name	Formula	Copies
WMM	N-phenyl-4-[(4H-1,2,4-triazol-3-ylsulfanyl)methyl]-1,3-thiazol-2-amine	C12 H11 N5 S2	2
CA	Calcium ion	Ca	4
ZN	Zinc ion	Zn	4

Water and common crystallization additives (EDO, NA) are not listed.

Primary citation

Discovery of Novel, Highly Potent, and Selective Matrix Metalloproteinase (MMP)-13 Inhibitors with a 1,2,4-Triazol-3-yl Moiety as a Zinc Binding Group Using a Structure-Based Design Approach. Nara, H., Kaieda, A., Sato, K. et al. J Med Chem (2017) 60:608-626. DOI 10.1021/acs.jmedchem.6b01007 · PubMed

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

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
2OW9 1.74 Å, Crystal structure analysis of the MMP13 catalytic domain in complex with specific…

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