8H78: Human MMP-2 catalytic domain

Crystal structure of human MMP-2 catalytic domain in complex with inhibitor. Determined by X-ray diffraction at 2.4 Å resolution. Released 18 Jan 2023.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,804
Mol. weight: 40.05 kDa
Ligands: L2U, 2HP, CA, ZN
Released: 18 Jan 2023

Explore 8H78 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H78 contains 6 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.

Chains A and B: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	15-20	6	2
β-strand	22	1	3
α-helix	29-44	16
β-strand	50-53	4	2
β-strand	61-66	6	2
β-strand	84-86	3	2
β-strand	97-100	4	2
β-strand	105-106	2	4
β-strand	113-114	2	4
α-helix	115-126	12
β-strand	129	1	1
α-helix	153-163	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Matrix metalloproteinase-2	A, B	protein	168	Homo sapiens	P08253 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8H78_1 Matrix metalloproteinase-2 (chains A, B)
MYNFFPRKPKWDKNQITYRIIGYTPDLAPETVDDAFARAFQVWSDVTPLRFSRIYDGEAD
IMINFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLGKGVGYSLFLVAA
HAFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASPD

Ligands and cofactors

ID	Name	Formula	Copies
L2U	(2~{R})-2-[[4-[(4-aminocarbonylphenyl)carbonylamino]phenyl]sulfonylamino]-5-[(2…	C41 H57 N9 O13 S	2
2HP	Dihydrogenphosphate ion	H2 O4 P	1
CA	Calcium ion	Ca	6
ZN	Zinc ion	Zn	4

Primary citation

Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with a Phenylbenzamide-Pentapeptide Hybrid Scaffold. Takeuchi, T., Nomura, Y., Tamita, T. et al. J Med Chem (2023) 66:822-836. DOI 10.1021/acs.jmedchem.2c01698 · PubMed

Other PDB entries of the same protein (UniProt P08253 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3AYU 2.0 Å, Crystal structure of MMP-2 active site mutant in complex with APP-drived decapeptide…
7XJO 2.0 Å, Crystal structure of human MMP-2 catalytic domain in complex with inhibitor
1GEN 2.15 Å, C-terminal domain of gelatinase a
1RTG 2.6 Å, C-terminal domain (haemopexin-like domain) of human matrix metalloproteinase-2
1EAK 2.66 Å, Catalytic domain of proMMP-2 E404Q mutant
1CK7 2.8 Å, Gelatinase a (full-length)
1QIB 2.8 Å, Crystal structure of gelatinase a catalytic domain
7XGJ 2.8 Å, Crystal structure of human MMP-2 catalytic domain in complex with inhibitor
1GXD 3.1 Å, proMMP-2/TIMP-2 complex
1CXW The second type II module from human matrix metalloproteinase 2
1HOV Solution structure of a catalytic domain of mmp-2 complexed with sc-74020
1J7M The Third Fibronectin Type II Module from Human Matrix Metalloproteinase 2

Browse structure collections

About this viewer

MolViewer shows 8H78 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.