MolNFT v1 · #47052 · protein
Structure of nagst-2
2ON5 · Na glutathione S-transferase 2: “Structure of nagst-2”. X-ray diffraction, 1 ligand (GSH), 17 pockets (best druggability 0.85). MolNFT v1 #47052 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ON5
- Type
- protein
- Length
- 1,648 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Na glutathione S-transferase 2
- Ligands
- GSH
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Na glutathione S-transferase 2 | protein | 206 | 61% helix, 9% strand | — |
Ligands and binding sites
- GSH · Glutathione · ligand · 8 copies · chains A, G, B, C, D, F, E, H
- EDO · 1,2-ethanediol · additive · 76 copies · chains A, D, G, B, E, C, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.85 | 0.87 | 110 | empty |
| 2 | 1126 | 0.84 | 0.85 | 90 | EDO, GSH |
| 3 | 1186 | 0.84 | 0.84 | 94 | EDO, GSH |
| 4 | 1159 | 0.83 | 0.84 | 100 | EDO, GSH |
| 5 | 1092 | 0.83 | 0.84 | 138 | EDO |
Interfaces
15 interfaces between chains.
- D–F · 1442 Ų buried · 21 hydrogen bonds · protein-protein
- E–H · 1427 Ų buried · 20 hydrogen bonds · protein-protein
- A–G · 1416 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1415 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 289 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2ON5 · Structure of NaGST-2 · 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
- Elsewhere: RCSB PDB 2ON5 · PDBe 2ON5
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