2D1O: Stromelysin-1

Stromelysin-1 (MMP-3) complexed to a hydroxamic acid inhibitor. Determined by X-ray diffraction at 2.02 Å resolution. Released 27 Jun 2006.

Method: X-ray diffraction
Resolution: 2.02 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,979
Mol. weight: 39.8 kDa
Ligands: FA4, CA, ZN
Released: 27 Jun 2006

Explore 2D1O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2D1O contains 8 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.

Chain A: 4 helices, 10 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	195-206	12
β-strand	209	1	1
β-strand	227	1	4
α-helix	229-231	3
α-helix	236-246	11

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	85	1	5
β-strand	96-101	6	6
α-helix	110-125	16
β-strand	131-134	4	6
β-strand	142-147	6	6
β-strand	165-167	3	6
β-strand	178-181	4	6
β-strand	186-187	2	7
β-strand	193-194	2	7
α-helix	195-207	13
β-strand	209	1	5
β-strand	227	1	4
α-helix	229-231	3
α-helix	236-246	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Stromelysin-1	A, B	protein	171	Homo sapiens	P08254 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2D1O_1 Stromelysin-1 (chains A, B)
FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADI
MISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHE
IGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPPDSP

Ligands and cofactors

ID	Name	Formula	Copies
FA4	SM-25453	C24 H42 N6 O3	2
CA	Calcium ion	Ca	6
ZN	Zinc ion	Zn	4

Primary citation

Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453. Kohno, T., Hochigai, H., Yamashita, E. et al. Biochem Biophys Res Commun (2006) 344:315-322. DOI 10.1016/j.bbrc.2006.03.098 · 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…

Browse structure collections

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