Research workbench
Anti-tryptase Fab E104.V1 bound to tryptase
Analyse Anti-tryptase Fab E104.V1 bound to tryptase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VVU
- Type
- protein
- Length
- 2,702 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptase ALPHA/BETA-1; Fab E104.V1 heavy chain; Fab E104.V1 light chain
- EC
- 3.4.21.59
- UniProt
- Q15661
- Ligands
- 0GJ, CA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 9 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptase ALPHA/BETA-1 (EC 3.4.21.59) | protein | 243 | 11% helix, 36% strand | Q15661 |
| B | Tryptase ALPHA/BETA-1 (EC 3.4.21.59) | protein | 244 | 11% helix, 36% strand | Q15661 |
| D, C | Tryptase ALPHA/BETA-1 (EC 3.4.21.59) | protein | 242 | 11% helix, 36% strand | Q15661 |
| E, H | Fab E104.V1 heavy chain | protein | 216 | 6% helix, 50% strand | — |
| F, I | Fab E104.V1 light chain | protein | 216 | 4% helix, 51% strand | — |
| G | Fab E104.V1 heavy chain | protein | 217 | 6% helix, 52% strand | — |
| J | Fab E104.V1 heavy chain | protein | 219 | 7% helix, 52% strand | — |
| K | Fab E104.V1 light chain | protein | 216 | 6% helix, 49% strand | — |
| L | Fab E104.V1 light chain | protein | 215 | 6% helix, 52% strand | — |
Ligands and binding sites
- 0GJ · L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide · ligand · 4 copies · chains A, B, D, C
- CA · Calcium ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.75 | 0.78 | 95 | empty |
| 2 | 825 | 0.73 | 0.78 | 81 | empty |
| 3 | 675 | 0.70 | 0.78 | 60 | empty |
| 4 | 666 | 0.69 | 0.77 | 51 | empty |
| 5 | 689 | 0.69 | 0.77 | 53 | empty |
Interfaces
26 interfaces between chains.
- J–K · 1859 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1797 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 1785 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1698 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1138 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 8 covalent (disulfide, covalent ligand).
Compared structures
- 6VVU · Anti-Tryptase fab E104.v1 bound to tryptase · the same entry in another collection · chain J against J, 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 6VVU · PDBe 6VVU · UniProt Q15661
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