2ZEC: Tryptase beta 2

Potent, Nonpeptide Inhibitors of Human Mast Cell Tryptase. Determined by X-ray diffraction at 2.06 Å resolution. Released 9 Dec 2008.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,313
Mol. weight: 110.45 kDa
Ligands: 11N
Released: 9 Dec 2008

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

Secondary structure: helices and β-sheets

2ZEC contains 41 α-helices and 101 β-strands across 4 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: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	41-50	10	3
β-strand	53-56	4	3
α-helix	58-60	3
β-strand	64	1	4
α-helix	68-70	3
β-strand	71-74	4	3
β-strand	79	1	5
β-strand	87-94	8	3
β-strand	108-112	5	3
α-helix	124-125	2
β-strand	126	1	2
α-helix	127-129	3
β-strand	140-144	5	2
β-strand	149	1	6
β-strand	152	1	6
α-helix	153-155	3
β-strand	159	1	5
β-strand	161-164	4	2
β-strand	167-168	2	2
α-helix	170-178	9
β-strand	181	1	7
β-strand	194-197	4	2
β-strand	203	1	1
β-strand	212-217	6	2
β-strand	220-229	10	2
β-strand	235	1	8
β-strand	238	1	8
β-strand	240-244	5	2
α-helix	245-248	4
α-helix	249-253	5

Chain B: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	9
β-strand	20-21	2	10
α-helix	22-23	2
β-strand	30-35	6	11
β-strand	41-50	10	11
β-strand	53-56	4	11
α-helix	58-60	3
β-strand	64	1	12
α-helix	68-70	3
β-strand	71-74	4	11
β-strand	79	1	13
β-strand	87-94	8	11
β-strand	108-112	5	11
α-helix	124-125	2
β-strand	126	1	10
α-helix	127-129	3
β-strand	140-144	5	10
β-strand	149	1	14
β-strand	152	1	14
α-helix	153-155	3
β-strand	159	1	13
β-strand	161-165	5	10
β-strand	167-168	2	10
α-helix	170-178	9
β-strand	181	1	15
β-strand	194-197	4	10
β-strand	203	1	9
α-helix	211	1
β-strand	212-217	6	10
β-strand	220-229	10	10
β-strand	235	1	16
β-strand	238	1	16
β-strand	240-244	5	10
α-helix	245-248	4
α-helix	249-253	5

Chain C: 12 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	17
β-strand	20-21	2	18
α-helix	22-23	2
β-strand	30-35	6	19
β-strand	41-50	10	19
β-strand	53-56	4	19
α-helix	58-60	3
β-strand	64	1	7
α-helix	65-67	3
α-helix	68-70	3
β-strand	71-74	4	19
β-strand	79	1	20
β-strand	87	1	19
β-strand	89-94	6	19
β-strand	108-112	5	19
α-helix	124-125	2
β-strand	126	1	18
α-helix	127-129	3
β-strand	139-144	6	18
β-strand	149	1	21
β-strand	152	1	21
α-helix	153-155	3
β-strand	159	1	20
β-strand	161-168	8	18
α-helix	170-178	9
β-strand	181	1	4
β-strand	194-197	4	18
β-strand	203	1	17
α-helix	211	1
β-strand	212-217	6	18
β-strand	220-229	10	18
β-strand	235	1	22
β-strand	238	1	22
α-helix	239	1
β-strand	240-244	5	18
α-helix	245-248	4
α-helix	249-253	5

Chain D: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	23
β-strand	20-21	2	24
α-helix	22-23	2
β-strand	30-35	6	25
β-strand	41-50	10	25
β-strand	53-56	4	25
α-helix	58-60	3
β-strand	64	1	15
α-helix	68-70	3
β-strand	71-74	4	25
β-strand	79	1	26
β-strand	87	1	25
β-strand	89-94	6	25
β-strand	108-112	5	25
α-helix	124-125	2
β-strand	126	1	24
α-helix	127-129	3
β-strand	140-144	5	24
β-strand	149	1	27
β-strand	152	1	27
α-helix	153-155	3
β-strand	159	1	26
α-helix	160	1
β-strand	161-164	4	24
β-strand	167-168	2	24
α-helix	170-177	8
β-strand	181	1	12
β-strand	194-197	4	24
β-strand	203	1	23
β-strand	212-217	6	24
β-strand	220-229	10	24
β-strand	235	1	28
β-strand	238	1	28
β-strand	240-244	5	24
α-helix	245-248	4
α-helix	249-255	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tryptase beta 2	A, B, C, D	protein	243	Homo sapiens	Q15661 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>2ZEC_1 Tryptase beta 2 (chains A, B, C, D)
IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQL
REQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFP
PGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDML
CAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHY
VPK

Ligands and cofactors

ID	Name	Formula	Copies
11N	1-[1'-(3-phenylacryloyl)spiro[1-benzofuran-3,4'-piperidin]-5-yl]methanamine	C22 H24 N2 O2	4

Primary citation

Potent, nonpeptide inhibitors of human mast cell tryptase. Synthesis and biological evaluation of novel spirocyclic piperidine amide derivatives. Costanzo, M.J., Yabut, S.C., Zhang, H.-C. et al. Bioorg Med Chem Lett (2008) 18:2114-2121. DOI 10.1016/j.bmcl.2008.01.093 · PubMed

Other PDB entries of the same protein (UniProt Q15661 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2F9N 1.6 Å, Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant K192Q/D216G in…
4MPU 1.65 Å, Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phen…
5F03 1.94 Å, TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylet…
4MPW 1.95 Å, Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di…
4MPX 2.0 Å, Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di…
2F9O 2.1 Å, Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant D216G
6O1F 2.15 Å, Complex between soybean trypsin inhibitor beta1-tryptase and a humanized fab
1LTO 2.2 Å, Human alpha1-tryptase
4MQA 2.25 Å, Human beta-tryptase co-crystal structure with {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bi…
2F9P 2.3 Å, Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant D216G in Complex with…
4MPV 2.31 Å, Human beta-tryptase co-crystal structure with (2R,4S)-N,N'-bis[3-({4-[3-(aminomethyl)phen…
8VGK 2.4 Å, CryoEM structure of tryptase in complex with engineered conformationally rigid…

Browse structure collections

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