1XUD: Matrix metalloproteinase-13

Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor. Determined by X-ray diffraction at 1.8 Å resolution. Released 26 Oct 2005.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,208
Mol. weight: 39.71 kDa
Ligands: PB4, CA, ZN
Released: 26 Oct 2005

Explore 1XUD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1XUD contains 9 α-helices and 18 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	106	1	1
α-helix	107-108	2
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	1	4
α-helix	256-266	11

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	106	1	4
β-strand	117-122	6	5
α-helix	131-146	16
β-strand	152-155	4	5
β-strand	163-168	6	5
β-strand	186-188	3	5
β-strand	199-202	4	5
α-helix	206	1
β-strand	207-208	2	6
β-strand	214-215	2	6
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	171	Homo sapiens	P45452 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1XUD_1 Collagenase 3 (chains A, B)
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADI
MISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHE
FGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN

Ligands and cofactors

ID	Name	Formula	Copies
PB4	N,n'-BIS(4-fluoro-3-methylbenzyl)pyrimidine-4,6-dicarboxamide	C22 H20 F2 N4 O2	2
CA	Calcium ion	Ca	4
ZN	Zinc ion	Zn	4

Primary citation

Structural basis for the highly selective inhibition of MMP-13. Engel, C.K., Pirard, B., Schimanski, S. et al. Chem Biol (2005) 12:181-189. DOI 10.1016/j.chembiol.2004.11.014 · 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

Browse structure collections

About this viewer

MolViewer shows 1XUD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.