2GDD: Human beta II tryptase with inhibitor CRA-27592

Human beta II tryptase with inhibitor CRA-27592. Determined by X-ray diffraction at 2.35 Å resolution. Released 11 Apr 2006.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,984
Mol. weight: 112.28 kDa
Ligands: 5AM
Released: 11 Apr 2006

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

Secondary structure: helices and β-sheets

2GDD contains 37 α-helices and 98 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: 10 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	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	83-90	8	3
β-strand	104-108	5	3
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-125	3
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	189	1	1
β-strand	198-203	6	2
β-strand	206-215	10	2
β-strand	221A	1	8
β-strand	224	1	8
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-239	5

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	39-48	10	11
β-strand	51-54	4	11
α-helix	56-58	3
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	135-140	6	10
β-strand	145	1	14
β-strand	149	1	14
α-helix	150-152	3
β-strand	154	1	13
β-strand	156-163	8	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
α-helix	225	1
β-strand	226-230	5	10
α-helix	232-234	3
α-helix	235-238	4

Chain C: 9 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	56-59	4
β-strand	60B	1	15
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
α-helix	111-114	4
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
β-strand	156-160	5	18
β-strand	162-163	2	18
α-helix	165-173	9
β-strand	173C	1	12
β-strand	180-183	4	18
β-strand	189	1	17
β-strand	198-202	5	18
β-strand	207-215	9	18
β-strand	221A	1	22
β-strand	224	1	22
β-strand	226-230	5	18
α-helix	231-234	4
α-helix	235-238	4

Chain D: 9 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	39-48	10	25
β-strand	51-54	4	25
α-helix	56-59	4
β-strand	60B	1	7
α-helix	61-63	3
β-strand	64-67	4	25
β-strand	72	1	26
β-strand	83-90	8	25
β-strand	104-108	5	25
β-strand	122	1	24
α-helix	123-125	3
β-strand	135-140	6	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	156-163	8	24
α-helix	165-173	9
β-strand	173C	1	4
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	232-234	3
α-helix	235-239	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tryptase beta-2	A, B, C, D	protein	245	Homo sapiens	P20231 (AlphaFold model)

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

>2GDD_1 Tryptase beta-2 (chains A, B, C, D)
IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQL
REQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFP
PGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDML
CAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHY
VPKKP

Ligands and cofactors

ID	Name	Formula	Copies
5AM	Benzyl {(1S)-5-amino-1-[(S)-HYDROXY(5-{[4-(4-phenylbutanoyl)piperazin-1-yl]meth…	C31 H42 N6 O5	4

Primary citation

Human beta II tryptase with inhibitor CRA-27592. Somoza, J.R. To be published.

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…
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
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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