MolNFT v1 · #100195 · protein
Human beta-tryptase co-crystal structure with {(1,1,3,3- tetramethyldisiloxane-1,3-DIYL)BIS[5-(METHYLSULFANYL)BENZENE-3,1- DIYL]}BIS({4-[3-(AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}METHANONE)
4MQA · Tryptase ALPHA/BETA-1: “Human beta-tryptase co-crystal structure with {(1,1,3,3…”. X-ray diffraction, 2 ligands (X00, SO4), 5 pockets (best druggability 0.55). MolNFT v1 #100195 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4MQA
- 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
- X00, SO4
- Pockets
- 5 · best druggability 0.55
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
- X00 · {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) · ligand · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.55 | 0.74 | 59 | SO4, X00 |
| 2 | 70 | 0.41 | 0.80 | 15 | empty |
| 3 | 56 | 0.31 | 0.76 | 14 | empty |
| 4 | 60 | 0.28 | 0.73 | 13 | empty |
| 5 | 54 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1120 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4MQA · Human beta-tryptase co-crystal structure with {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis… · 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 4MQA · PDBe 4MQA · UniProt Q15661
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