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… 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 v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptase beta-2
- EC
- 3.4.21.59
- UniProt
- P20231
- Ligands
- 5TA
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 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.
| Volume (ų) | 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 Ų 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-chloro-pyridin-3-yleth… · 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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