7XGJ: Human MMP-2 catalytic domain

Crystal structure of human MMP-2 catalytic domain in complex with inhibitor. Determined by X-ray diffraction at 2.8 Å resolution. Released 29 Jun 2022.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 4,210
Mol. weight: 60.14 kDa
Ligands: ZN, CA
Released: 29 Jun 2022

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

Secondary structure: helices and β-sheets

7XGJ contains 13 α-helices and 32 β-strands across 6 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	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	84-87	4	2
α-helix	88	1
β-strand	97-100	4	2
α-helix	104	1
β-strand	105-106	2	4
β-strand	113-114	2	4
α-helix	115-126	12
β-strand	129-130	2	1
α-helix	153-163	11

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
β-strand	15-20	6	6
β-strand	22	1	3
α-helix	29-46	18
β-strand	50-53	4	6
β-strand	61-66	6	6
β-strand	84-87	4	6
α-helix	88	1
β-strand	97-100	4	6
β-strand	105-106	2	7
β-strand	113-114	2	7
α-helix	115-126	12
β-strand	129	1	5
α-helix	153-163	11

Chain C: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	8
β-strand	15-20	6	9
α-helix	29-44	16
β-strand	50-53	4	9
β-strand	61-66	6	9
β-strand	84-87	4	9
α-helix	88	1
β-strand	97-100	4	9
β-strand	105-106	2	10
β-strand	113-114	2	10
α-helix	115-126	12
β-strand	129	1	8
α-helix	154-163	10

Chains D, E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4-5	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Matrix metalloproteinase-2	A, B, C	protein	168	Homo sapiens	P08253 (AlphaFold model)
Gzs-asn-asp-ala-leu-iml-eoe-NH2	D, E, F	protein	8	synthetic construct

Sequence of entity 1 (A, B, C), FASTA

>7XGJ_1 Matrix metalloproteinase-2 (chains A, B, C)
MYNFFPRKPKWDKNQITYRIIGYTPDLAPETVDDAFARAFQVWSDVTPLRFSRIYDGEAD
IMINFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLGKGVGYSLFLVAA
HAFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASPD

Sequence of entity 2 (D, E, F), FASTA

>7XGJ_2 GZS-ASN-ASP-ALA-LEU-IML-EOE-NH2 (chains D, E, F)
XNDALIXX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
CA	Calcium ion	Ca	9

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…
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
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
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

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