Research workbench
Structure-function analysis of human L-prostaglandin D synthase bound with fatty acid
Analyse Structure-function analysis of human L-prostaglandin D synthase bound with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O2Y
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin-H2 D-isomerase
- EC
- 5.3.99.2
- UniProt
- P41222
- Ligands
- OLA, PLM
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin-H2 D-isomerase (EC 5.3.99.2) | protein | 160 | 20% helix, 48% strand | P41222 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.75 | 0.83 | 44 | OLA, PLM |
| 2 | 432 | 0.74 | 0.83 | 36 | OLA, PLM |
| 3 | 321 | 0.52 | 0.74 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 536 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3O2Y · Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid · the same entry in another collection · chain A against A, TM-score 1.00
- P41222 · AlphaFold monomer V2.0 prediction for prostaglandin-H2 D-isomerase (P41222) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P41222
- Elsewhere: RCSB PDB 3O2Y · PDBe 3O2Y · UniProt P41222
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