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The structural basis of aspirin activity inferred from the crystal structure of inactivated prostaglandin H2 synthase
Analyse The structural basis of aspirin activity inferred from the crystal structure of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PTH
- Type
- protein
- Length
- 1,102 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin H2 synthase-1
- EC
- 1.14.99.1
- Ligands
- HEM, SAL, NAG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin H2 synthase-1 (EC 1.14.99.1) | protein | 551 | 45% helix, 9% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- SAL · 2-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.82 | 0.83 | 114 | BOG, SAL |
| 2 | 1143 | 0.81 | 0.82 | 101 | BOG |
| 3 | 702 | 0.77 | 0.82 | 66 | empty |
| 4 | 77 | 0.71 | 0.95 | 19 | SAL |
| 5 | 405 | 0.65 | 0.78 | 39 | HEM |
Interfaces
1 interface between chains.
- A–B · 2522 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 1PTH · The Structural Basis of Aspirin Activity Inferred from the Crystal Structure of… · 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 1PTH · PDBe 1PTH
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