3V7T: Human Beta-Tryptase

Crystal Structure of Human Beta-Tryptase Complexed with a Synthetic Inhibitor with a Tropanylamide Scaffold. Determined by X-ray diffraction at 2.09 Å resolution. Released 14 Mar 2012.

Method: X-ray diffraction
Resolution: 2.09 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,360
Mol. weight: 112.07 kDa
Ligands: CO3, 0GX
Released: 14 Mar 2012

Explore 3V7T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V7T contains 42 α-helices and 99 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	30-36	7	3
β-strand	40-50	11	3
β-strand	53-56	4	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
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
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: 11 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	58-61	4
β-strand	64	1	12
α-helix	65-67	3
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
α-helix	160	1
β-strand	161-164	4	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
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: 11 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	30-36	7	19
β-strand	40-50	11	19
β-strand	53-56	4	19
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	87-94	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
α-helix	160	1
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
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	249-255	7

Chain D: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	23
β-strand	20-21	2	24
α-helix	22-23	2
β-strand	30-36	7	25
β-strand	40-50	11	25
β-strand	53-56	4	25
α-helix	58-61	4
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	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
α-helix	239	1
β-strand	240-244	5	24
α-helix	245-248	4
α-helix	249-253	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TPSB2 protein	A, B, C, D	protein	245	Homo sapiens	P20231 (AlphaFold model)

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

>3V7T_1 TPSB2 protein (chains A, B, C, D)
IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQL
REQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFP
PGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDML
CAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHY
VPKKP

Ligands and cofactors

ID	Name	Formula	Copies
CO3	Carbonate ion	C O3	2
0GX	{(3-exo)-3-[5-(aminomethyl)-2-fluorophenyl]-8-azabicyclo[3.2.1]oct-8-yl}(4-brom…	C23 H28 Br F N2 O2 S	4

Primary citation

A beta-tryptase inhibitor with a tropanylamide scaffold to improve in vitro stability and to lower hERG channel binding affinity. Liang, G., Choi-Sledeski, Y.M., Shum, P. et al. Bioorg Med Chem Lett (2012) 22:1606-1610. DOI 10.1016/j.bmcl.2011.12.127 · PubMed

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

9QFU 1.98 Å, Human Tryptase beta-2 (hTPSB2) complexed with covalent inhibitor Compound #1
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)
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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