7XJO: Human MMP-2 catalytic domain

Crystal structure of human MMP-2 catalytic domain in complex with inhibitor. Determined by X-ray diffraction at 2.0 Å resolution. Released 29 Jun 2022.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,044
Mol. weight: 40.68 kDa
Ligands: ZN, CA, B3P
Released: 29 Jun 2022

Explore 7XJO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XJO contains 7 α-helices and 20 β-strands across 4 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: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	15-20	6	2
α-helix	29-44	16
β-strand	50-53	4	2
β-strand	61-66	6	2
β-strand	84-87	4	2
α-helix	88	1
β-strand	97-100	4	2
β-strand	105-106	2	3
β-strand	113-114	2	3
α-helix	115-126	12
β-strand	129	1	1
α-helix	153-163	11

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	4
β-strand	15-20	6	5
α-helix	29-44	16
β-strand	50-53	4	5
β-strand	61-66	6	5
β-strand	84-87	4	5
β-strand	97-100	4	5
β-strand	105-106	2	6
β-strand	113-114	2	6
α-helix	115-127	13
β-strand	129	1	4
α-helix	153-163	11

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	5-6	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Matrix metalloproteinase-2	A, B	protein	168	Homo sapiens	P08253 (AlphaFold model)
Ryh-kfb-glu-asp-dab-leu-eme-eoe-NH2	C, D	protein	9	synthetic construct

Sequence of entity 1 (A, B), FASTA

>7XJO_1 Matrix metalloproteinase-2 (chains A, B)
MYNFFPRKPKWDKNQITYRIIGYTPDLAPETVDDAFARAFQVWSDVTPLRFSRIYDGEAD
IMINFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLGKGVGYSLFLVAA
HAFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASPD

Sequence of entity 2 (C, D), FASTA

>7XJO_2 RYH-KFB-GLU-ASP-DAB-LEU-EME-EOE-NH2 (chains C, D)
XXEDALXXX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
CA	Calcium ion	Ca	7
B3P	2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-pr…	C11 H26 N2 O6	1

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

Primary citation

Discovery of Aryloxyphenyl-Heptapeptide Hybrids as Potent and Selective Matrix Metalloproteinase-2 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis. Takeuchi, T., Hayashi, M., Tamita, T. et al. J Med Chem (2022) 65:8493-8510. DOI 10.1021/acs.jmedchem.2c00613 · 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…
1GEN 2.15 Å, C-terminal domain of gelatinase a
8H78 2.4 Å, Crystal structure of human MMP-2 catalytic domain in complex with inhibitor
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

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