MolNFT v1 · #21042 · protein
Structure of prostaglandin F synthase with prostaglandin D2
1RY0 · Aldo-keto reductase family 1 member C3: “Structure of prostaglandin F synthase with prostaglandin D2”. X-ray diffraction, 2 ligands (NAP, PG2), 4 pockets (best druggability 0.80). MolNFT v1 #21042 on GenesisL1: 3D structure, binding…
- PDB
- 1RY0
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldo-keto reductase family 1 member C3
- EC
- 1.1.1.-, 1.3.1.20, 1.1.1.188
- UniProt
- P42330
- Ligands
- NAP, PG2
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aldo-keto reductase family 1 member C3 (EC 1.1.1.-, 1.3.1.20, 1.1.1.188) | protein | 319 | 41% helix, 17% strand | P42330 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- PG2 · Prostaglandin D2 · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.80 | 0.84 | 65 | NAP, PG2 |
| 2 | 637 | 0.80 | 0.84 | 60 | NAP, PG2 |
| 3 | 433 | 0.65 | 0.78 | 56 | empty |
| 4 | 68 | 0.27 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 446 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1RY0 · Structure of prostaglandin F synthase with prostaglandin D2 · the same entry in another collection · chain A against A, TM-score 1.00
- P42330 · AlphaFold monomer V2.0 prediction for aldo-keto reductase family 1 member C3 (P42330) · 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 P42330
- Elsewhere: RCSB PDB 1RY0 · PDBe 1RY0 · UniProt P42330
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