Research workbench
Human beta tryptase II complexed with activated ketone inhibitor cra- 29382
Analyse Human beta tryptase II complexed with activated ketone inhibitor cra- 29382 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FXR
- Type
- protein
- Length
- 972 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptase beta-2
- EC
- 3.4.21.59
- UniProt
- P20231
- Ligands
- C3A
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tryptase beta-2 (EC 3.4.21.59) | protein | 243 | 10% helix, 35% strand | P20231 |
Ligands and binding sites
- C3A · Allyl {(1S)-1-[(5-{4-[(2,3-dihydro-1H-inden-2-ylamino)carbonyl]benzyl}-1,2,4-oxadiazol-3-yl)carbonyl]-3-pyrrolidin-3-ylpropyl}carbamate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.50 | 0.75 | 30 | empty |
| 2 | 202 | 0.49 | 0.75 | 33 | empty |
| 3 | 169 | 0.43 | 0.74 | 39 | empty |
| 4 | 72 | 0.42 | 0.81 | 23 | C3A |
| 5 | 107 | 0.40 | 0.76 | 29 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1138 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1131 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 460 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 429 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 2FXR · human beta tryptase II complexed with activated ketone inhibitor CRA-29382 · 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 2FXR · PDBe 2FXR · UniProt P20231
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