Research workbench

Human beta tryptase II with inhibitor cra-28427

Analyse Human beta tryptase II with inhibitor cra-28427 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FS9
Type: protein
Length: 972 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tryptase beta-2
EC: 3.4.21.59
UniProt: P20231
Ligands: C4A
Pockets: 7 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Tryptase beta-2 (EC 3.4.21.59)	protein	243	10% helix, 37% strand	P20231

Ligands and binding sites

C4A · Ethyl {(1S)-5-amino-1-[(5-{4-[(2,3-dihydro-1H-inden-2-ylamino)carbonyl]benzyl}-1,2,4-oxadiazol-3-yl)carbonyl]pentyl}carbamate · ligand · 4 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	197	0.48	0.75	33	empty
2	206	0.47	0.74	31	empty
3	105	0.40	0.77	31	C4A
4	84	0.38	0.77	22	empty
5	84	0.30	0.73	15	empty

Interfaces

4 interfaces between chains.

B–C · 1146 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1141 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 446 Å² buried · 1 hydrogen bond · protein-protein
A–B · 434 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

2FS9 · Human beta tryptase II with inhibitor CRA-28427 · 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 2FS9 · PDBe 2FS9 · UniProt P20231

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.