4DPE: MMP3

Structure of MMP3 complexed with a platinum-based inhibitor. Determined by X-ray diffraction at 1.96 Å resolution. Released 20 Feb 2013.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,863
Mol. weight: 40.89 kDa
Ligands: ZN, CA, PT, NGH
Released: 20 Feb 2013

Explore 4DPE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DPE contains 6 α-helices and 17 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	85	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	209	1	1
α-helix	236-246	11

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	96-101	6	4
α-helix	110-125	16
β-strand	131-134	4	4
β-strand	142-147	6	4
β-strand	165-167	3	4
β-strand	178-181	4	4
β-strand	186-187	2	5
β-strand	193-194	2	5
α-helix	195-206	12
α-helix	236-246	11
β-strand	254	1	2

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>4DPE_1 Stromelysin-1 (chains A, B)
FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADI
MISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHE
IGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPPDSPET

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
CA	Calcium ion	Ca	6
PT	Platinum (II) ion	Pt	6
NGH	N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid	C13 H20 N2 O5 S	1

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

Primary citation

Structure of matrix metalloproteinase-3 with a platinum-based inhibitor. Belviso, B.D., Caliandro, R., Siliqi, D. et al. Chem Commun (Camb) (2013) 49:5492-5494. DOI 10.1039/c3cc41278d · 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
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…
1CQR 2.0 Å, Crystal structure of the stromelysin catalytic domain at 2.0 a resolution

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