1D7X: MMP3

Crystal structure of MMP3 complexed with a modified proline scaffold based inhibitor. Determined by X-ray diffraction at 2.0 Å resolution. Released 23 Oct 2000.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,947
Mol. weight: 40.03 kDa
Ligands: SPC, CA, ZN
Released: 23 Oct 2000

Explore 1D7X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D7X contains 6 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: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	84	1	1
β-strand	96-101	6	2
α-helix	110-125	16
β-strand	131-134	4	2
β-strand	142-147	6	2
β-strand	165-167	3	2
β-strand	178-181	4	2
β-strand	186-187	2	3
β-strand	193-194	2	3
α-helix	195-207	13
β-strand	210	1	1
α-helix	236-246	11

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	584-585	2	4
β-strand	596-601	6	5
α-helix	610-625	16
β-strand	631-634	4	5
β-strand	642-647	6	5
β-strand	665-667	3	5
β-strand	678-681	4	5
β-strand	686-687	2	6
β-strand	693-694	2	6
α-helix	695-706	12
β-strand	709-710	2	4
α-helix	736-746	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Stromelysin-1 precursor	A, B	protein	173	Homo sapiens	P08254 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1D7X_1 STROMELYSIN-1 PRECURSOR (chains A, B)
FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADI
MISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHE
IGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPPDSPET

Ligands and cofactors

ID	Name	Formula	Copies
SPC	N-hydroxy 1N(4-methoxyphenyl)sulfonyl-4-(z,e-N-methoxyimino)pyrrolidine-2R-carb…	C13 H19 N3 O6 S	2
CA	Calcium ion	Ca	6
ZN	Zinc ion	Zn	4

Primary citation

Design, synthesis, and biological evaluation of matrix metalloproteinase inhibitors derived from a modified proline scaffold. Cheng, M., De, B., Almstead, N.G. et al. J Med Chem (1999) 42:5426-5436. DOI 10.1021/jm9904699 · PubMed

Other PDB entries of the same protein (UniProt P08254 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1HY7 1.5 Å, A carboxylic acid based inhibitor in complex with MMP3
1CIZ 1.64 Å, X-ray structure of human stromelysin catalytic domain complexes with non-peptide…
1HFS 1.7 Å, Crystal structure of the catalytic domain of human fibroblast stromelysin-1 inhibited…
1CAQ 1.8 Å, X-ray structure of human stromelysin catalytic domain complexes with non-peptide…
1USN 1.8 Å, Crystal structure of the catalytic domain of human fibroblast stromelysin-1 inhibited…
1C3I 1.83 Å, Human stromelysin-1 catalytic domain complexed with ro-26-2812
4G9L 1.88 Å, Structure of MMP3 complexed with NNGH inhibitor.
1G49 1.9 Å, A carboxylic acid based inhibitor in complex with MMP3
1SLM 1.9 Å, Crystal structure of fibroblast stromelysin-1: the C-truncated human proenzyme
4DPE 1.96 Å, Structure of MMP3 complexed with a platinum-based inhibitor.
4JA1 1.96 Å, Structure of MMP3 complexed with a platinum-based inhibitor
1B8Y 2.0 Å, X-ray structure of human stromelysin catalytic domain complexed with non-peptide…

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