MolNFT v1 · #71251 · protein
Crystal structure of a possible gutathione S-tranferase from rhodopseudomonas palustris
3M8N · Possible glutathione S-transferase: “Crystal structure of a possible gutathione S-tranferase from rhodopseudomonas palustris”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.77). MolNFT v1 #71251 on GenesisL1: 3D…
- PDB
- 3M8N
- Type
- protein
- Length
- 802 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Possible glutathione S-transferase
- EC
- 2.5.1.18
- UniProt
- Q6N1S2
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Possible glutathione S-transferase (EC 2.5.1.18) | protein | 204 | 51% helix, 9% strand | Q6N1S2 |
| B | Possible glutathione S-transferase (EC 2.5.1.18) | protein | 183 | 48% helix, 10% strand | Q6N1S2 |
| C | Possible glutathione S-transferase (EC 2.5.1.18) | protein | 193 | 52% helix, 8% strand | Q6N1S2 |
| D | Possible glutathione S-transferase (EC 2.5.1.18) | protein | 222 | 49% helix, 9% strand | Q6N1S2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.77 | 0.81 | 73 | empty |
| 2 | 269 | 0.73 | 0.87 | 50 | empty |
| 3 | 448 | 0.67 | 0.79 | 60 | empty |
| 4 | 356 | 0.64 | 0.79 | 36 | empty |
| 5 | 93 | 0.54 | 0.84 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1489 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1470 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1020 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 652 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 154 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 3M8N · Crystal structure of a possible gutathione S-tranferase from Rhodopseudomonas palustris · the same entry in another collection · chain C against C, 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 Q6N1S2
- Elsewhere: RCSB PDB 3M8N · PDBe 3M8N · UniProt Q6N1S2
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