2BM2: Human beta-II tryptase

human beta-II tryptase in complex with 4-(3-Aminomethyl-phenyl)- piperidin-1-yl-(5-phenethyl- pyridin-3-yl)-methanone. Determined by X-ray diffraction at 2.2 Å resolution. Released 22 Mar 2005.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 8,145
Mol. weight: 111.56 kDa
Ligands: PM2
Released: 22 Mar 2005

Explore 2BM2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2BM2 contains 36 α-helices and 102 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	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-48	10	3
β-strand	51-54	4	3
α-helix	56-59	4
β-strand	60B	1	4
α-helix	61-63	3
β-strand	64-67	4	3
β-strand	72	1	5
β-strand	83	1	3
β-strand	85-90	6	3
β-strand	104-108	5	3
α-helix	120-121	2
β-strand	122	1	2
α-helix	123	1
β-strand	136-140	5	2
β-strand	145	1	6
β-strand	149	1	6
α-helix	150-152	3
β-strand	154	1	5
β-strand	156-160	5	2
β-strand	162-163	2	2
α-helix	165-173	9
β-strand	173C	1	7
β-strand	180-183	4	2
β-strand	185	1	8
β-strand	188	1	8
β-strand	189	1	1
β-strand	198-203	6	2
β-strand	206-215	10	2
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-239	5

Chain B: 8 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	39-48	10	11
β-strand	51-54	4	11
α-helix	56-59	4
β-strand	60B	1	12
α-helix	61-63	3
β-strand	64-67	4	11
β-strand	72	1	13
β-strand	83-90	8	11
β-strand	104-108	5	11
β-strand	122	1	10
α-helix	123-125	3
β-strand	136-140	5	10
β-strand	145	1	14
β-strand	149	1	14
α-helix	150-152	3
β-strand	154	1	13
β-strand	156-159	4	10
β-strand	162-163	2	10
α-helix	165-171	7
β-strand	173C	1	15
β-strand	180-183	4	10
β-strand	189	1	9
β-strand	198-203	6	10
β-strand	206-215	10	10
β-strand	221A	1	16
β-strand	224	1	16
β-strand	226-230	5	10
α-helix	231-234	4
α-helix	235-239	5

Chain C: 10 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	39-48	10	19
β-strand	51-54	4	19
α-helix	56-58	3
β-strand	60B	1	7
α-helix	60C-60D	2
α-helix	61-63	3
β-strand	64-67	4	19
β-strand	72	1	20
β-strand	83-90	8	19
β-strand	104-108	5	19
β-strand	122	1	18
α-helix	123-125	3
β-strand	136-140	5	18
β-strand	145	1	21
β-strand	149	1	21
α-helix	150-152	3
β-strand	154	1	20
α-helix	155	1
β-strand	156-160	5	18
β-strand	162-163	2	18
α-helix	165-173	9
β-strand	173C	1	4
β-strand	180-183	4	18
β-strand	189	1	17
β-strand	198-203	6	18
β-strand	206-215	10	18
β-strand	221A	1	22
β-strand	224	1	22
β-strand	226-230	5	18
α-helix	232-234	3
α-helix	235-241	7

Chain D: 9 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	39-48	10	25
β-strand	51-54	4	25
α-helix	56-59	4
β-strand	60B	1	15
α-helix	61-63	3
β-strand	64-68	5	25
β-strand	72	1	26
β-strand	83	1	25
β-strand	85-90	6	25
β-strand	104-108	5	25
β-strand	122	1	24
α-helix	123-125	3
β-strand	136-140	5	24
β-strand	145	1	27
β-strand	149	1	27
α-helix	150-152	3
β-strand	154	1	26
α-helix	155	1
β-strand	156-159	4	24
β-strand	162-163	2	24
α-helix	165-172	8
β-strand	173C	1	12
β-strand	180-183	4	24
β-strand	189	1	23
β-strand	198-202	5	24
β-strand	207-215	9	24
β-strand	221A	1	28
β-strand	224	1	28
β-strand	226-230	5	24
α-helix	231-234	4
α-helix	235-241	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human BETA2 tryptase	A, B, C, D	protein	245	HOMO SAPIENS	P20231 (AlphaFold model)

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

>2BM2_1 HUMAN BETA2 TRYPTASE (chains A, B, C, D)
IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQL
REQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFP
PGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDML
CAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHY
VPKKP

Ligands and cofactors

ID	Name	Formula	Copies
PM2	1-[3-(1-{[5-(2-phenylethyl)pyridin-3-yl]carbonyl}piperidin-4-yl)phenyl]methanam…	C26 H29 N3 O	4

Primary citation

Structure Based Design of 4-(3-Aminomethylphenyl) Piperidinyl-1-Amides: Novel, Potent, Selective, and Orally Bioavailable Inhibitors of Bii Tryptase. Levell, J., Astles, P., Eastwood, P. et al. Bioorg Med Chem (2005) 13:2859. DOI 10.1016/J.BMC.2005.02.014 · 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)
3V7T 2.09 Å, Crystal Structure of Human Beta-Tryptase Complexed with a Synthetic Inhibitor with a…
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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