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Human beta-II tryptase in complex with 4-(3-aminomethyl-phenyl)- piperidin-1-yl-(5-phenethyl- pyridin-3-yl)-methanone

Analyse Human beta-II tryptase in complex with 4-(3-aminomethyl-phenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BM2
Type: protein
Length: 968 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human BETA2 tryptase
EC: 3.4.21.59
UniProt: P20231
Ligands: PM2
Pockets: 11 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Human BETA2 tryptase (EC 3.4.21.59)	protein	242	10% helix, 36% strand	P20231

Ligands and binding sites

PM2 · 1-[3-(1-{[5-(2-phenylethyl)pyridin-3-yl]carbonyl}piperidin-4-yl)phenyl]methanamine · ligand · 4 copies · chains A, C, B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	280	0.57	0.77	32	empty
2	260	0.54	0.76	37	empty
3	97	0.39	0.77	24	PM2
4	62	0.36	0.79	15	PM2
5	79	0.34	0.76	22	PM2

Interfaces

4 interfaces between chains.

A–C · 1116 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 1099 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 436 Å² buried · 1 hydrogen bond · protein-protein
B–C · 388 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

2BM2 · human beta-II tryptase in complex with 4-(3-Aminomethyl-phenyl)… · the same entry in another collection · chain A against A, TM-score 1.00
P20231 · AlphaFold monomer V2.0 prediction for tryptase beta-2 (P20231) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P20231
Elsewhere: RCSB PDB 2BM2 · PDBe 2BM2 · UniProt P20231

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