Research workbench
X-ray crystal structure of prostaglandin F synthase from leishmania major friedlin bound to NADPH
Analyse X-ray crystal structure of prostaglandin F synthase from leishmania major… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G5D
- Type
- protein
- Length
- 565 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin F2-alpha SYNTHASE/D-arabinose dehydrogenase
- EC
- 1.1.1.188
- UniProt
- Q4Q646
- Ligands
- NDP
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin F2-alpha SYNTHASE/D-arabinose dehydrogenase (EC 1.1.1.188) | protein | 283 | 44% helix, 16% strand | Q4Q646 |
| B | Prostaglandin F2-alpha SYNTHASE/D-arabinose dehydrogenase (EC 1.1.1.188) | protein | 282 | 44% helix, 16% strand | Q4Q646 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.64 | 0.83 | 35 | NDP |
| 2 | 218 | 0.63 | 0.82 | 37 | NDP |
Interfaces
1 interface between chains.
- A–B · 164 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4G5D · X-ray crystal structure of Prostaglandin f synthase from Leishmania major Friedlin bound… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q4Q646
- Elsewhere: RCSB PDB 4G5D · PDBe 4G5D · UniProt Q4Q646
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