5BPA: Collagenase 3

X-RAY Co-structure of MMP-13 with 4-[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}formamido)methyl]benzoate. Determined by X-ray diffraction at 1.79 Å resolution. Released 17 Jun 2015.

Method: X-ray diffraction
Resolution: 1.79 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,032
Mol. weight: 39.87 kDa
Ligands: ZN, CA, 4UF
Released: 17 Jun 2015

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

Secondary structure: helices and β-sheets

5BPA contains 11 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: 6 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
α-helix	206	1
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	216-227	12
β-strand	230	1	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

>5BPA_1 Collagenase 3 (chains A, B)
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADI
MISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHE
FGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
CA	Calcium ion	Ca	6
4UF	4-{[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}carbonyl)am…	C24 H22 N4 O5	2

Primary citation

Fragment-based discovery of indole inhibitors of matrix metalloproteinase-13. Taylor, S.J., Abeywardane, A., Liang, S. et al. J Med Chem (2011) 54:8174-8187. DOI 10.1021/jm201129m · 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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