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Crystal structure of human tryptase with potent non-peptide inhibitor
Analyse Crystal structure of human tryptase with potent non-peptide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZA5
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptase beta 2
- EC
- 3.4.21.59
- UniProt
- Q6B052
- Ligands
- 2FF
- Pockets
- 13 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tryptase beta 2 (EC 3.4.21.59) | protein | 242 | 11% helix, 36% strand | Q6B052 |
Ligands and binding sites
- 2FF · (5-(aminomethyl)-2H-spiro[benzofuran-3,4'-piperidine]-1'-yl)(5-(phenylethynyl)furan-2-yl)methanone · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.55 | 0.76 | 32 | empty |
| 2 | 273 | 0.54 | 0.76 | 34 | empty |
| 3 | 146 | 0.48 | 0.78 | 35 | 2FF |
| 4 | 131 | 0.45 | 0.77 | 20 | 2FF |
| 5 | 115 | 0.44 | 0.78 | 21 | 2FF |
Interfaces
4 interfaces between chains.
- B–D · 1116 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1113 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 437 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 428 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 2ZA5 · Crystal Structure of human tryptase with potent non-peptide inhibitor · 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 Q6B052
- Elsewhere: RCSB PDB 2ZA5 · PDBe 2ZA5 · UniProt Q6B052
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