6HV2: MMP-13

MMP-13 in complex with the peptide IMISF. Determined by X-ray diffraction at 1.71 Å resolution. Released 30 Jan 2019.

Method: X-ray diffraction
Resolution: 1.71 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,469
Mol. weight: 19.86 kDa
Ligands: ZN, CA
Released: 30 Jan 2019

Explore 6HV2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HV2 contains 3 α-helices and 9 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: 3 helices, 8 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	184-188	5	1
β-strand	199-202	4	1
β-strand	207-208	2	2
β-strand	214-215	2	2
α-helix	216-227	12
β-strand	243	1	1
α-helix	256-266	11

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	164-165	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Collagenase 3	A	protein	168	Homo sapiens	P45452 (AlphaFold model)
Collagenase 3	B	protein	5	Homo sapiens	P45452 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6HV2_1 Collagenase 3 (chains A)
EYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIAD
IMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAH
EFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGD

Sequence of entity 2 (B), FASTA

>6HV2_2 Collagenase 3 (chains B)
IMISF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	3

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

Primary citation

Drug Design Inspired by Nature: Crystallographic Detection of an Auto-Tailored Protease Inhibitor Template. Gall, F.M., Hohl, D., Frasson, D. et al. Angew Chem Int Ed Engl (2019) 58:4051-4055. DOI 10.1002/anie.201812348 · 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
2OW9 1.74 Å, Crystal structure analysis of the MMP13 catalytic domain in complex with specific…

Browse structure collections

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