MolNFT v1 · #102642 · protein
Three-dimensional structure of the C65A-K59A double mutant of human lipocalin-type prostaglandin D synthase holo-form
4ORX · Prostaglandin-H2 D-isomerase: “Three-dimensional structure of the C65A-K59A double mutant of human lipocalin-type prostaglandin D synthase…”. X-ray diffraction, 2 ligands (PEU, SO4), 1 pocket (best druggability 0.85). MolNFT v1…
- PDB
- 4ORX
- Type
- protein
- Length
- 318 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
- PEU, SO4
- Pockets
- 1 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin-H2 D-isomerase (EC 5.3.99.2) | protein | 159 | 19% helix, 48% strand | P41222 |
Ligands and binding sites
- PEU · 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56, 59,62,65,68,71,74,77,80-heptacosaoxadooctacontan-82-ol · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.85 | 0.85 | 79 | PEU |
Interfaces
1 interface between chains.
- A–B · 404 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4ORX · Three-dimensional structure of the C65A-K59A double mutant of Human lipocalin-type… · 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 4ORX · PDBe 4ORX · UniProt P41222
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