2ZEB: Tryptase beta 2

Potent, Nonpeptide Inhibitors of Human Mast Cell Tryptase. Determined by X-ray diffraction at 2.5 Å resolution. Released 9 Dec 2008.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,063
Mol. weight: 110.76 kDa
Ligands: 11M
Released: 9 Dec 2008

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

Secondary structure: helices and β-sheets

2ZEB contains 40 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, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	5-6	2	2
α-helix	7-8	2
β-strand	15-20	6	3
β-strand	26-35	10	3
β-strand	38-41	4	3
α-helix	43-46	4
β-strand	49	1	4
α-helix	53-55	3
β-strand	56-59	4	3
β-strand	64	1	5
β-strand	72	1	3
β-strand	74-79	6	3
β-strand	93-97	5	3
α-helix	109-110	2
β-strand	111	1	2
α-helix	112-114	3
β-strand	125-129	5	2
β-strand	134	1	6
β-strand	137	1	6
α-helix	138-140	3
β-strand	144	1	5
β-strand	146-149	4	2
β-strand	152-153	2	2
α-helix	155-163	9
β-strand	166	1	7
β-strand	179-182	4	2
β-strand	188	1	1
β-strand	197-202	6	2
β-strand	205-214	10	2
β-strand	220	1	8
β-strand	223	1	8
β-strand	225-229	5	2
α-helix	231-233	3
α-helix	234-238	5

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	9
β-strand	5-6	2	10
α-helix	7-8	2
β-strand	15-20	6	11
β-strand	26-35	10	11
β-strand	38-41	4	11
α-helix	43-45	3
β-strand	49	1	12
α-helix	53-55	3
β-strand	56-59	4	11
β-strand	64	1	13
β-strand	72-79	8	11
β-strand	93-97	5	11
α-helix	109-110	2
β-strand	111	1	10
α-helix	112-114	3
β-strand	125-129	5	10
β-strand	134	1	14
β-strand	137	1	14
α-helix	138-140	3
β-strand	144	1	13
β-strand	146-149	4	10
β-strand	152-153	2	10
α-helix	155-163	9
β-strand	166	1	15
β-strand	179-182	4	10
β-strand	188	1	9
β-strand	197-202	6	10
β-strand	205-214	10	10
β-strand	225-229	5	10
α-helix	230-233	4
α-helix	234-238	5

Chain C: 11 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	16
β-strand	5-6	2	17
α-helix	7-8	2
β-strand	15-20	6	18
β-strand	26-35	10	18
β-strand	38-41	4	18
α-helix	43-45	3
β-strand	49	1	7
α-helix	50-51	2
α-helix	53-55	3
β-strand	56-60	5	18
β-strand	64	1	19
α-helix	69	1
β-strand	72	1	18
β-strand	74-79	6	18
β-strand	93-97	5	18
α-helix	109-110	2
β-strand	111	1	17
α-helix	112-114	3
β-strand	122	1	17
β-strand	125-129	5	17
β-strand	134	1	20
β-strand	137	1	20
α-helix	138-140	3
β-strand	144	1	19
β-strand	146-149	4	17
β-strand	152-153	2	17
α-helix	155-163	9
β-strand	166	1	4
β-strand	179-182	4	17
β-strand	188	1	16
β-strand	197-201	5	17
β-strand	206-214	9	17
β-strand	220	1	21
β-strand	223	1	21
β-strand	225-229	5	17
α-helix	230-233	4
α-helix	234-238	5

Chain D: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	22
β-strand	5-6	2	23
α-helix	7-8	2
β-strand	15-20	6	24
β-strand	26-35	10	24
β-strand	38-41	4	24
α-helix	43-45	3
β-strand	49	1	15
α-helix	53-55	3
β-strand	56-59	4	24
β-strand	64	1	25
β-strand	72-79	8	24
β-strand	93-97	5	24
α-helix	109-110	2
β-strand	111	1	23
α-helix	112-114	3
β-strand	125-129	5	23
β-strand	134	1	26
β-strand	137	1	26
α-helix	138-140	3
β-strand	144	1	25
α-helix	145	1
β-strand	146-149	4	23
β-strand	152-153	2	23
α-helix	155-163	9
β-strand	166	1	12
β-strand	179-182	4	23
β-strand	188	1	22
α-helix	196	1
β-strand	197-202	6	23
β-strand	205-214	10	23
β-strand	220	1	27
β-strand	223	1	27
β-strand	225-229	5	23
α-helix	230-233	4
α-helix	234-240	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

>2ZEB_1 Tryptase beta 2 (chains A, B, C, D)
IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQL
REQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFP
PGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDML
CAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHY
VPK

Ligands and cofactors

ID	Name	Formula	Copies
11M	1-(1'-{[3-(methylsulfanyl)-2-benzothiophen-1-yl]carbonyl}spiro[1-benzofuran-3,4…	C23 H24 N2 O2 S2	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…
2ZEC 2.06 Å, Potent, Nonpeptide Inhibitors of Human Mast Cell Tryptase
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…

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