Research workbench
Crystal structure of human beta-tryptase complexed with a synthetic inhibitor with a tropanylamide scaffold
Analyse Crystal structure of human beta-tryptase complexed with a synthetic inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V7T
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TPSB2 protein
- UniProt
- Q6NZY1
- Ligands
- 0GX, CO3
- Pockets
- 10 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | TPSB2 protein | protein | 242 | 10% helix, 36% strand | Q6NZY1 |
Ligands and binding sites
- 0GX · {(3-exo)-3-[5-(aminomethyl)-2-fluorophenyl]-8-azabicyclo[3.2.1]oct-8-yl}(4-bromo-3-methyl-5-propoxythiophen-2-yl)methanone · ligand · 4 copies · chains A, C, B, D
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.54 | 0.75 | 34 | empty |
| 2 | 80 | 0.46 | 0.81 | 15 | empty |
| 3 | 198 | 0.45 | 0.74 | 38 | 0GX, CO3 |
| 4 | 100 | 0.39 | 0.76 | 27 | 0GX, CO3 |
| 5 | 62 | 0.37 | 0.79 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1130 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1117 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 489 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 478 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3V7T · Crystal Structure of Human Beta-Tryptase Complexed with a Synthetic Inhibitor with a… · the same entry in another collection · 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 Q6NZY1
- Elsewhere: RCSB PDB 3V7T · PDBe 3V7T · UniProt Q6NZY1
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