MolNFT v1 · #18171 · protein
Prostaglandin H2 synthase-1 complexed with P-(2'-iodo-5'-thenoyl) hydrotropic acid (iodosuprofen)
1PGE: “Prostaglandin H2 synthase-1 complexed with P-(2'-iodo-5'-thenoyl) hydrotropic acid (iodosuprofen)”. X-ray diffraction, 3 ligands (HEM, ISF, NAG), 12 pockets (best druggability 0.82). MolNFT v1 #18171 on GenesisL1: 3D structure…
- PDB
- 1PGE
- 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, ISF, NAG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin H2 synthase-1 (EC 1.14.99.1) | protein | 551 | 46% helix, 9% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ISF · P-(2'-iodo-5'-thenoyl)hydrotropic 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
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.82 | 0.87 | 76 | empty |
| 2 | 384 | 0.79 | 0.88 | 46 | empty |
| 3 | 710 | 0.78 | 0.82 | 64 | empty |
| 4 | 252 | 0.77 | 0.89 | 42 | BOG, ISF |
| 5 | 233 | 0.76 | 0.90 | 39 | BOG, ISF |
Interfaces
1 interface between chains.
- A–B · 2526 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 1PGE · Prostaglandin H2 synthase-1 complexed with P-(2'-iodo-5'-THENOYL)HYDROTROPIC acid… · 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 1PGE · PDBe 1PGE
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