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Crystal structure of the recombinant human alpha I tryptase mutant K192Q/D216G in complex with leupeptin
Analyse Crystal structure of the recombinant human alpha I tryptase mutant K192Q/D216G… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F9N
- Type
- protein
- Length
- 984 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha I tryptase; Leupeptin
- EC
- 3.4.21.59
- UniProt
- P15157
- Ligands
- ACE, NAG, FUC
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha I tryptase (EC 3.4.21.59) | protein | 243 | 11% helix, 35% strand | P15157 |
| E, F, G, H | Leupeptin | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies
- 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.56 | 0.81 | 38 | empty |
| 2 | 121 | 0.51 | 0.80 | 27 | empty |
| 3 | 216 | 0.48 | 0.74 | 42 | empty |
| 4 | 177 | 0.45 | 0.74 | 31 | empty |
| 5 | 128 | 0.42 | 0.76 | 21 | empty |
Interfaces
14 interfaces between chains.
- B–C · 1316 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1315 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 603 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 595 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 362 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 covalent, 4 glycan, 4 modified (disulfide, covalent ligand, N-glycosylation, nonstandard).
Compared structures
- 2F9N · Crystal Structure of the Recombinant Human Alpha I Tryptase Mutant K192Q/D216G in Complex… · 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 2F9N · PDBe 2F9N · UniProt P15157
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