Research workbench
Crystal structure of the recombinant human alpha I tryptase mutant D216G in complex with leupeptin
Analyse Crystal structure of the recombinant human alpha I tryptase mutant D216G in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F9P
- Type
- protein
- Length
- 983 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptase alpha-1; Leupeptin
- EC
- 3.4.21.59
- Ligands
- ACE, NAG, FUC
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Tryptase alpha-1 (EC 3.4.21.59) | protein | 243 | 9% helix, 36% strand | — |
| E, F, G, H | Leupeptin | protein | 3 | 0% helix, 33% strand | — |
| D | Tryptase alpha-1 (EC 3.4.21.59) | protein | 242 | 9% helix, 36% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, E, B, F, C, G, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D, B
- FUC · alpha-L-fucopyranose · sugar
- BU3 · (R,R)-2,3-butanediol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.66 | 0.77 | 83 | empty |
| 2 | 269 | 0.52 | 0.75 | 47 | empty |
| 3 | 70 | 0.51 | 0.85 | 23 | empty |
| 4 | 123 | 0.43 | 0.76 | 16 | empty |
| 5 | 73 | 0.35 | 0.76 | 17 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1305 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1288 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 623 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 590 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 351 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 covalent, 4 modified, 2 glycan (disulfide, covalent ligand, nonstandard, N-glycosylation).
Compared structures
- 2F9P · Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant D216G in Complex with… · 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
- Elsewhere: RCSB PDB 2F9P · PDBe 2F9P
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