MolNFT v1 · #67432 · protein
Human GST A1-1-gimf with gsdhn
3IK9 · Glutathione S-transferase A1: “Human GST A1-1-gimf with gsdhn”. X-ray diffraction, 1 ligand (BOB), 20 pockets (best druggability 0.85). MolNFT v1 #67432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IK9
- Type
- protein
- Length
- 1,751 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase A1
- EC
- 2.5.1.18
- UniProt
- P08263
- Ligands
- BOB
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, H | Glutathione S-transferase A1 (EC 2.5.1.18) | protein | 219 | 59% helix, 7% strand | P08263 |
| B | Glutathione S-transferase A1 (EC 2.5.1.18) | protein | 221 | 61% helix, 7% strand | P08263 |
| F | Glutathione S-transferase A1 (EC 2.5.1.18) | protein | 216 | 60% helix, 7% strand | P08263 |
Ligands and binding sites
- BOB · (S)-2-amino-5-((R)-1-(carboxymethylamino)-3-((3S,4R)-1,4-dihydroxynonan-3-ylthio)-1-oxopropan-2-ylamino)-5-oxopentanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.85 | 0.89 | 100 | BOB |
| 2 | 1136 | 0.84 | 0.84 | 118 | BOB |
| 3 | 1083 | 0.83 | 0.84 | 104 | BOB |
| 4 | 1200 | 0.81 | 0.82 | 112 | BOB |
| 5 | 304 | 0.73 | 0.86 | 41 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1510 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1497 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1471 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1458 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 260 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3IK9 · Human GST A1-1-GIMF with GSDHN · 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 P08263
- Elsewhere: RCSB PDB 3IK9 · PDBe 3IK9 · UniProt P08263
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