Research workbench
CryoEM structure of tryptase in complex with wild type anti-tryptase Fab E104.v1
Analyse CryoEM structure of tryptase in complex with wild type anti-tryptase Fab E104.v1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8VGH
- Type
- protein
- Length
- 2,668 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens
- Molecule
- Tryptase alpha/beta-1; Fab E104.v1 light chain; Fab E104.v1 heavy chain
- EC
- 3.4.21.59
- UniProt
- Q15661
- Pockets
- 20 · best druggability 0.69
Structure
electron microscopy · resolution 2.9 · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tryptase alpha/beta-1 (EC 3.4.21.59) | protein | 243 | 9% helix, 35% strand | Q15661 |
| G, E, I, L | Fab E104.v1 light chain | protein | 213 | 6% helix, 51% strand | — |
| H, F, J, K | Fab E104.v1 heavy chain | protein | 211 | 8% helix, 47% strand | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.69 | 0.78 | 52 | empty |
| 2 | 645 | 0.69 | 0.77 | 52 | empty |
| 3 | 111 | 0.68 | 0.91 | 24 | empty |
| 4 | 546 | 0.68 | 0.78 | 47 | empty |
| 5 | 541 | 0.68 | 0.78 | 40 | empty |
Interfaces
24 interfaces between chains.
- J–I · 1700 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1700 Ų buried · 14 hydrogen bonds · protein-protein
- F–E · 1696 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 1696 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1084 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 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 0.99
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 8VGH · PDBe 8VGH · UniProt Q15661
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