MolNFT v1 · #141128 · protein
Crystal structure of hematopoietic prostaglandin D synthase in complex with U004
5YX1: “Crystal structure of hematopoietic prostaglandin D synthase in complex with U004”. X-ray diffraction, 3 ligands (GSH, UX4, MG). MolNFT v1 #141128 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YX1
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- O60760
- Ligands
- GSH, UX4, MG
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | — | protein | 198 | — | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
- UX4 · ethyl 4-[(8R)-3,8-dimethyl-4-oxo-4,6,7,8,9,10-hexahydrothieno[2',3':4,5]pyrimido[1,2-a]azepin-2-yl]carbamoylpiperazine-1-carboxylate · ligand · 3 copies · chains B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5YX1 · Crystal structure of hematopoietic prostaglandin D synthase in complex with U004 · the same entry in another collection · chain A against A, TM-score 1.00
- O60760 · AlphaFold monomer V2.0 prediction for hematopoietic prostaglandin D synthase (O60760) · 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 O60760
- Elsewhere: RCSB PDB 5YX1 · PDBe 5YX1 · UniProt O60760
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