MolNFT v1 · #102643 · protein
Three-dimensional structure of the C65A-K59A double mutant of human lipocalin-type prostaglandin D synthase holo, second crystal form
4ORY · Prostaglandin-H2 D-isomerase: “Three-dimensional structure of the C65A-K59A double mutant of human lipocalin-type prostaglandin D synthase…”. X-ray diffraction, 1 ligand (PEU), 12 pockets (best druggability 0.85). MolNFT v1 #102643…
- PDB
- 4ORY
- Type
- protein
- Length
- 1,288 residues
- Chains
- 8
- 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
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 20% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin-H2 D-isomerase (EC 5.3.99.2) | protein | 159 | 22% helix, 48% strand | P41222 |
| B | Prostaglandin-H2 D-isomerase (EC 5.3.99.2) | protein | 161 | 17% helix, 47% strand | P41222 |
| C, E | Prostaglandin-H2 D-isomerase (EC 5.3.99.2) | protein | 160 | 19% helix, 49% strand | P41222 |
| D | Prostaglandin-H2 D-isomerase (EC 5.3.99.2) | protein | 157 | 20% helix, 47% strand | P41222 |
| F | Prostaglandin-H2 D-isomerase (EC 5.3.99.2) | protein | 167 | 19% helix, 46% strand | P41222 |
| G | Prostaglandin-H2 D-isomerase (EC 5.3.99.2) | protein | 166 | 20% helix, 46% strand | P41222 |
| H | Prostaglandin-H2 D-isomerase (EC 5.3.99.2) | protein | 158 | 20% 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 · 2 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.85 | 0.86 | 75 | PEU |
| 2 | 1178 | 0.84 | 0.85 | 82 | PEU |
| 3 | 768 | 0.82 | 0.85 | 59 | empty |
| 4 | 785 | 0.81 | 0.84 | 50 | empty |
| 5 | 1091 | 0.79 | 0.81 | 103 | empty |
Interfaces
11 interfaces between chains.
- E–F · 420 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 420 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 419 Ų buried · 10 hydrogen bonds · protein-protein
- E–G · 407 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 407 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4ORY · Three-dimensional structure of the C65A-K59A double mutant of Human lipocalin-type… · the same entry in another collection · chain H against H, TM-score 1.00
- P41222 · AlphaFold monomer V2.0 prediction for prostaglandin-H2 D-isomerase (P41222) · a predicted model of the same protein · chain C 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 4ORY · PDBe 4ORY · UniProt P41222
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