Research workbench
Human beta-tryptase co-crystal structure with [(1,1,3,3- tetramethyldisiloxane-1,3-DIYL)DI-1-benzofuran-3,5-DIYL]BIS({4-[3- (AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}METHANONE)
Analyse Human beta-tryptase co-crystal structure with [(1,1,3,3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MPW
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptase ALPHA/BETA-1
- EC
- 3.4.21.59
- UniProt
- Q15661
- Ligands
- 2AJ, CL
- Pockets
- 5 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tryptase ALPHA/BETA-1 (EC 3.4.21.59) | protein | 243 | 11% helix, 35% strand | Q15661 |
Ligands and binding sites
- 2AJ · [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzofuran-3,5-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) · ligand · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.41 | 0.77 | 30 | empty |
| 2 | 53 | 0.34 | 0.79 | 16 | ACT |
| 3 | 73 | 0.33 | 0.75 | 14 | empty |
| 4 | 53 | 0.29 | 0.75 | 14 | empty |
| 5 | 82 | 0.28 | 0.71 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1106 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4MPW · Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di… · the same entry in another collection · chain A against A, TM-score 1.00
- Q15661 · AlphaFold monomer V2.0 prediction for tryptase ALPHA/BETA-1 (Q15661) · 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 Q15661
- Elsewhere: RCSB PDB 4MPW · PDBe 4MPW · UniProt Q15661
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