Research workbench

TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid

Analyse TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyrid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F03
Type: protein
Length: 485 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.94
Source: Homo sapiens
Molecule: Tryptase beta-2
EC: 3.4.21.59
UniProt: P20231
Ligands: 5TA
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · resolution 1.94 · 2 distinct chains · 11% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tryptase beta-2 (EC 3.4.21.59)	protein	242	11% helix, 35% strand	P20231
B	Tryptase beta-2 (EC 3.4.21.59)	protein	243	11% helix, 35% strand	P20231

Ligands and binding sites

5TA · (5~{S})-5-[[3-(aminomethyl)phenoxy]methyl]-3-[3-[2-(2-chloranylpyridin-3-yl)ethynyl]phenyl]-1,3-oxazolidin-2-one · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	194	0.51	0.77	31	empty
2	58	0.42	0.83	22	empty
3	143	0.41	0.74	28	empty

Interfaces

1 interface between chains.

A–B · 459 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5F03 · Tryptase B2 in complex with 5-(3-aminomethyl-phenoxymethyl)-3-[3-(2… · 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 5F03 · PDBe 5F03 · UniProt P20231

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