6N9D: Stromelysin-1

Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) mutant (L34G/L133P/L151C/G154A) with matrix metalloproteinase-3 catalytic domain (MMP-3cd). Determined by X-ray diffraction at 2.67 Å resolution. Released 15 May 2019.

Method: X-ray diffraction
Resolution: 2.67 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,675
Mol. weight: 39.51 kDa
Ligands: ZN, CA
Released: 15 May 2019

Explore 6N9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N9D contains 11 α-helices and 22 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	96-101	6	1
α-helix	112-125	14
β-strand	131-134	4	1
β-strand	142-147	6	1
β-strand	162-167	6	1
β-strand	178-181	4	1
β-strand	186-187	2	2
β-strand	193-194	2	2
α-helix	195-207	13
β-strand	222	1	1
α-helix	236-246	11

Chain B: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	5-7	3
α-helix	8-14	7
β-strand	17-23	7	3
β-strand	28	1	4
β-strand	35-39	5	4
β-strand	40-47	8	3
β-strand	60-64	5	4
α-helix	67-69	3
β-strand	83-87	5	3
β-strand	88-90	3	4
β-strand	93-95	3	4
β-strand	101-104	4	3
α-helix	105-107	3
α-helix	110-116	7
α-helix	121-124	4
β-strand	128-131	4	5
β-strand	144-147	4	5
α-helix	154-157	4
α-helix	159-163	5
β-strand	164-170	7	6
β-strand	173-178	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Stromelysin-1	A	protein	165	Homo sapiens	P08254 (AlphaFold model)
Metalloproteinase inhibitor 1	B	protein	184	Homo sapiens	P01033 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6N9D_1 Stromelysin-1 (chains A)
FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADI
MISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHE
IGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYG

Sequence of entity 2 (B), FASTA

>6N9D_2 Metalloproteinase inhibitor 1 (chains B)
CTCVPPHPQTAFCNSDLVIRAKFVGTPEVNQTTGYQRYEIKMTKMYKGFQALGDAADIRF
VYTPAMESVCGYFHRSHNRSEEFLIAGKLQDGLLHITTCSFVAPWNSLSLAQRRGFTKTY
TVGCEECTVFPCPSIPCKLQSGTHCLWTDQCLQASEKGFQSRHLACLPREPGLCTWQSLR
SQIA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	3

Primary citation

Directed evolution of the metalloproteinase inhibitor TIMP-1 reveals that its N- and C-terminal domains cooperate in matrix metalloproteinase recognition. Raeeszadeh-Sarmazdeh, M., Greene, K.A., Sankaran, B. et al. J Biol Chem (2019) 294:9476-9488. DOI 10.1074/jbc.RA119.008321 · 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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