3KMC: TNF-alpha-converting enzyme

Crystal structure of catalytic domain of TACE with tartrate-based inhibitor. Determined by X-ray diffraction at 1.8 Å resolution. Released 22 Dec 2009.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,284
Mol. weight: 62.12 kDa
Ligands: 403, INN, ZN
Released: 22 Dec 2009

Explore 3KMC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KMC contains 24 α-helices and 24 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: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	224-231	8	1
α-helix	233-238	6
α-helix	244-264	21
β-strand	276-284	9	1
α-helix	288-290	3
α-helix	314-324	11
α-helix	326-329	4
β-strand	334-339	6	1
α-helix	344-346	3
β-strand	349-351	3	1
β-strand	368-371	4	2
β-strand	376-379	4	2
β-strand	382-386	5	1
β-strand	388-389	2	3
β-strand	392-393	2	3
α-helix	394-395	2
α-helix	396-411	16
α-helix	415-417	3
α-helix	427-429	3
α-helix	445-448	4
α-helix	452-459	8
α-helix	462-469	8
β-strand	471	1	1

Chain B: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	224-231	8	4
α-helix	233-238	6
α-helix	244-263	20
β-strand	276-284	9	4
β-strand	289	1	5
β-strand	300	1	5
α-helix	314-324	11
α-helix	326-329	4
β-strand	334-339	6	4
α-helix	344-346	3
β-strand	349-351	3	4
β-strand	368-371	4	6
β-strand	376-379	4	6
β-strand	382-386	5	4
β-strand	388-389	2	7
β-strand	392-393	2	7
α-helix	394-395	2
α-helix	396-410	15
α-helix	415-417	3
β-strand	421	1	8
β-strand	424	1	8
α-helix	427-429	3
α-helix	445-448	4
α-helix	452-469	18
β-strand	471	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TNF-alpha-converting enzyme	A, B	protein	270	Homo sapiens	P78536 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3KMC_1 TNF-alpha-converting enzyme (chains A, B)
RADPDPMKNTCKLLVVADHRFYRYMGRGEESTTTNYLIELIDRVDDIYRNTAWDNAGFKG
YGIQIEQIRILKSPQEVKPGEKHYNMAKSYPNEEKDAWDVKMLLEQFSFDIAEEASKVCL
AHLFTYQDFDMGTLGLAYGGSPRANSHGGVCPKAYYSPVGKKNIYLNSGLTSTKNYGKTI
LTKEADLVTTHELGHNFGAEHDPDGLAECAPNEDQGGKYVMYPIAVSGDHENNKMFSQCS
KQSIYKTIESKAQECFQERSNKGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
403	(2R,3R)-4-[4-(2-chlorophenyl)piperazin-1-yl]-2,3-dihydroxy-4-oxo-N-(2-thiophen-…	C20 H24 Cl N3 O4 S	1
INN	N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(…	C19 H37 N5 O5	1
ZN	Zinc ion	Zn	2

Primary citation

The discovery of novel tartrate-based TNF-alpha converting enzyme (TACE) inhibitors. Rosner, K.E., Guo, Z., Orth, P. et al. Bioorg Med Chem Lett (2009) 20:1189-1193. DOI 10.1016/j.bmcl.2009.12.004 · PubMed

Other PDB entries of the same protein (UniProt P78536 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2DDF 1.7 Å, Crystal structure of TACE in complex with TAPI-2
8CQY 1.7 Å, Crystal structure of the PTPN3 PDZ domain bound to the PBM TACE C-terminal peptide
3L0V 1.75 Å, Crystal structure of catalytic domain of TACE with the first hydantoin inhibitor…
3EWJ 1.8 Å, Crystal structure of catalytic domain of TACE with carboxylate inhibitor
3KME 1.85 Å, Crystal structure of catalytic domain of TACE with phenyl-pyrrolidinyl-tartrate inhibitor
3LE9 1.85 Å, Crystal structure of the catalytic domain of TACE with Indazolinone-phenyl-hydantoin…
3O64 1.88 Å, Crystal structure of catalytic domain of TACE with 2-(2-Aminothiazol-4-yl)pyrrolidine-Bas…
2I47 1.9 Å, Crystal structure of catalytic domain of TACE with inhibitor
3E8R 1.9 Å, Crystal structure of catalytic domain of TACE with hydroxamate inhibitor
3EDZ 1.9 Å, Crystal structure of catalytic domain of TACE with hydroxamate inhibitor
3LGP 1.9 Å, Crystal structure of catalytic domain of tace with benzimidazolyl-thienyl-tartrate based…
3L0T 1.92 Å, Crystal structure of catalytic domain of TACE with hydantoin inhibitor

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