Research workbench
Crystal structure of the recombinant human alpha I tryptase mutant D216G
Analyse Crystal structure of the recombinant human alpha I tryptase mutant D216G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F9O
- Type
- protein
- Length
- 970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptase alpha-1
- EC
- 3.4.21.59
- UniProt
- P15157
- Ligands
- NAG, FUC
- Pockets
- 14 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tryptase alpha-1 (EC 3.4.21.59) | protein | 242 | 11% helix, 36% strand | P15157 |
| C, D | Tryptase alpha-1 (EC 3.4.21.59) | protein | 243 | 11% helix, 36% strand | P15157 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.55 | 0.76 | 39 | empty |
| 2 | 289 | 0.54 | 0.75 | 35 | empty |
| 3 | 122 | 0.44 | 0.77 | 29 | empty |
| 4 | 108 | 0.43 | 0.78 | 24 | empty |
| 5 | 97 | 0.38 | 0.76 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1144 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1140 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 522 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2F9O · Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant D216G · 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 P15157
- Elsewhere: RCSB PDB 2F9O · PDBe 2F9O · UniProt P15157
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