Research workbench
Structure of prostaglandin synthase D of nilaparvata lugens
Analyse Structure of prostaglandin synthase D of nilaparvata lugens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H5L
- Type
- protein
- Length
- 395 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase S2
- UniProt
- J9Q529
- Ligands
- GSH
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase S2 | protein | 196 | 60% helix, 10% strand | J9Q529 |
| B | Glutathione S-transferase S2 | protein | 199 | 60% helix, 10% strand | J9Q529 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.79 | 0.80 | 81 | GSH, PEG, EDO |
| 2 | 99 | 0.40 | 0.76 | 18 | empty |
| 3 | 92 | 0.40 | 0.77 | 19 | empty |
| 4 | 69 | 0.32 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1447 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5H5L · Structure of prostaglandin synthase D of Nilaparvata lugens · 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 J9Q529
- Elsewhere: RCSB PDB 5H5L · PDBe 5H5L · UniProt J9Q529
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