MolNFT v1 · #31548 · protein
2.0 ångström crystal structure of manganese protoporphyrin IX- reconstituted ovine prostaglandin H2 synthase-1 complexed with flurbiprofen
2AYL · Prostaglandin G/H synthase 1: “2.0 ångström crystal structure of manganese protoporphyrin IX- reconstituted ovine prostaglandin H2…”. X-ray diffraction, 4 ligands (FLP, MNH, NAG), 9 pockets (best druggability 0.86). MolNFT v1 #31548…
- PDB
- 2AYL
- Type
- protein
- Length
- 1,106 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin G/H synthase 1
- EC
- 1.14.99.1
- UniProt
- P05979
- Ligands
- FLP, MNH, NAG, MAN
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin G/H synthase 1 (EC 1.14.99.1) | protein | 553 | 46% helix, 9% strand | P05979 |
Ligands and binding sites
- FLP · Flurbiprofen · ligand · 2 copies · chains A, B
- MNH · Manganese protoporphyrin IX · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains B, A
- BOG · octyl beta-D-glucopyranoside · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.86 | 0.87 | 124 | empty |
| 2 | 258 | 0.78 | 0.90 | 38 | BOG, FLP |
| 3 | 629 | 0.78 | 0.84 | 76 | GOL |
| 4 | 261 | 0.77 | 0.89 | 40 | BOG, FLP |
| 5 | 414 | 0.67 | 0.79 | 43 | MNH, GOL |
Interfaces
1 interface between chains.
- A–B · 2624 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 2AYL · 2.0 Angstrom Crystal Structure of Manganese Protoporphyrin IX-reconstituted Ovine… · 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 2AYL · PDBe 2AYL · UniProt P05979
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