Research workbench
The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1
Analyse The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PRH
- Type
- protein
- Length
- 1,108 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
- UniProt
- P05979
- Ligands
- HEM
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin H2 synthase-1 (EC 1.14.99.1) | protein | 554 | 47% helix, 9% strand | P05979 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.81 | 0.86 | 78 | empty |
| 2 | 125 | 0.78 | 0.96 | 22 | empty |
| 3 | 355 | 0.78 | 0.88 | 45 | empty |
| 4 | 288 | 0.77 | 0.89 | 43 | empty |
| 5 | 629 | 0.77 | 0.83 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 2572 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1PRH · The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1 · the same entry in another collection · chain A against A, TM-score 1.00
- P05979 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 1 (P05979) · a predicted model of the same protein · 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 P05979
- Elsewhere: RCSB PDB 1PRH · PDBe 1PRH · UniProt P05979
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