9QFU: Human Tryptase beta-2

Human Tryptase beta-2 (hTPSB2) complexed with covalent inhibitor Compound #1. Determined by X-ray diffraction at 1.98 Å resolution. Released 26 Mar 2025.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,818
Mol. weight: 114.42 kDa
Ligands: A1I52
Released: 26 Mar 2025

Explore 9QFU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QFU contains 43 α-helices and 97 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: 12 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	115-118	4
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
α-helix	160	1
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
α-helix	211	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	249-255	7

Chain B: 9 helices, 24 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	139-144	6	10
β-strand	149	1	14
β-strand	152	1	14
α-helix	153-155	3
β-strand	159	1	13
β-strand	161-168	8	10
α-helix	170-178	9
β-strand	181	1	15
β-strand	194-197	4	10
β-strand	203	1	9
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: 10 helices, 24 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	68-70	3
β-strand	71-74	4	19
β-strand	79	1	20
β-strand	87-94	8	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
β-strand	240-244	5	18
α-helix	245-248	4
α-helix	249-253	5

Chain D: 12 helices, 24 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	87-94	8	25
β-strand	108-112	5	25
α-helix	115-118	4
α-helix	124-125	2
β-strand	126	1	24
α-helix	127-129	3
β-strand	139-144	6	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	161-168	8	24
α-helix	170-178	9
β-strand	181	1	12
β-strand	194-197	4	24
β-strand	203	1	23
α-helix	211	1
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	P20231 (AlphaFold model)

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

>9QFU_1 Tryptase beta-2 (chains A, B, C, D)
IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQL
REQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFP
PGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDML
CAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHY
VPK

Ligands and cofactors

ID	Name	Formula	Copies
A1I52	~{N}-[(1~{S},2~{S})-6-azanyl-1-[5-[[4-[2-(3,4-dichlorophenyl)ethoxy]phenyl]meth…	C30 H31 Cl2 F N4 O4	4

Water and common crystallization additives (SO4, PEG, EDO, ACT, GOL) are not listed.

Primary citation

Integrating Surface Plasmon Resonance and Docking Analysis for Mechanistic Insights of Tryptase Inhibitors. Porta, A., Manelfi, C., Talarico, C. et al. Molecules (2025) 30. DOI 10.3390/molecules30061338 · PubMed

Other PDB entries of the same protein (UniProt P20231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FPZ 2.0 Å, Human tryptase with 2-amino benzimidazole
4A6L 2.05 Å, beta-tryptase inhibitor
9QFV 2.06 Å, Human Tryptase beta-2 (hTPSB2)
3V7T 2.09 Å, Crystal Structure of Human Beta-Tryptase Complexed with a Synthetic Inhibitor with a…
2BM2 2.2 Å, human beta-II tryptase in complex with 4-(3-Aminomethyl-phenyl)-…
2FWW 2.25 Å, human beta-tryptase II complexed with 4-piperidinebutyrate to make acylenzyme
2FS9 2.3 Å, Human beta tryptase II with inhibitor CRA-28427
2ZA5 2.3 Å, Crystal Structure of human tryptase with potent non-peptide inhibitor
2GDD 2.35 Å, Human beta II tryptase with inhibitor CRA-27592
2FS8 2.5 Å, Human beta-tryptase II with inhibitor CRA-29382
2FXR 2.5 Å, human beta tryptase II complexed with activated ketone inhibitor CRA-29382
1A0L 3.0 Å, Human beta-tryptase: a ring-like tetramer with active sites facing a central pore

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