2YIG: MMP13

MMP13 in complex with a novel selective non zinc binding inhibitor. Determined by X-ray diffraction at 1.7 Å resolution. Released 29 Jun 2011.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 3,024
Mol. weight: 39.87 kDa
Ligands: 5EL, ZN, CA
Released: 29 Jun 2011

Explore 2YIG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YIG contains 10 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	105-106	2	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: 5 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
α-helix	206	1
β-strand	207-208	2	7
β-strand	214-215	2	7
α-helix	216-228	13
β-strand	230-231	2	1
α-helix	256-266	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Collagenase 3	A, B	protein	171	HOMO SAPIENS	P45452 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2YIG_1 COLLAGENASE 3 (chains A, B)
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADI
MISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHE
FGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN

Ligands and cofactors

ID	Name	Formula	Copies
5EL	4-(4-{[(3S)-3-hydroxy-1-AZABICYCLO[2.2.2]OCT-3-yl]ethynyl}phenoxy)-N-(pyridin-4…	C28 H27 N3 O3	2
ZN	Zinc ion	Zn	4
CA	Calcium ion	Ca	4

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

Primary citation

Selective Non Zinc Binding Inhibitors of Mmp13. Savi, C.D., Morley, A.D., Ting, A. et al. Bioorg Med Chem Lett (2011) 21:4215. DOI 10.1016/J.BMCL.2011.05.075 · 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
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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