Research workbench
Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-BIS[3-({4- [3-(AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}CARBONYL)PHENYL]-8-hydroxy-6- (1-hydroxycyclobutyl)-5,7-DIOXASPIRO[3.4]OCTANE-6,8-dicarboxamide
Analyse Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-BIS[3-({4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MPU
- 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
- X2A, SO4
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tryptase ALPHA/BETA-1 (EC 3.4.21.59) | protein | 243 | 10% helix, 35% strand | Q15661 |
Ligands and binding sites
- X2A · (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide · ligand · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · 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 | 254 | 0.48 | 0.73 | 39 | X2A, SO4 |
| 2 | 56 | 0.35 | 0.79 | 14 | empty |
| 3 | 71 | 0.32 | 0.75 | 14 | empty |
| 4 | 68 | 0.32 | 0.75 | 15 | MES |
| 5 | 67 | 0.31 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1092 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4MPU · Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)pheny… · 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 4MPU · PDBe 4MPU · UniProt Q15661
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.