Research workbench
Crystal structure of human microsomal glutathione S-transferase 2
Analyse Crystal structure of human microsomal glutathione S-transferase 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SSS
- Type
- protein
- Length
- 786 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microsomal glutathione S-transferase 2
- EC
- 2.5.1.18
- UniProt
- Q99735
- Ligands
- M88, NA, K, SO4, SCN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Microsomal glutathione S-transferase 2 (EC 2.5.1.18) | protein | 136 | 84% helix, 0% strand | Q99735 |
| B, E | Microsomal glutathione S-transferase 2 (EC 2.5.1.18) | protein | 130 | 86% helix, 0% strand | Q99735 |
| C | Microsomal glutathione S-transferase 2 (EC 2.5.1.18) | protein | 133 | 86% helix, 0% strand | Q99735 |
| D | Microsomal glutathione S-transferase 2 (EC 2.5.1.18) | protein | 128 | 87% helix, 0% strand | Q99735 |
| F | Microsomal glutathione S-transferase 2 (EC 2.5.1.18) | protein | 129 | 87% helix, 0% strand | Q99735 |
Ligands and binding sites
- M88 · 1-(8Z-hexadecenoyl)-rac-glycerol · ligand · 5 copies · chains B, E, F, C
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · chains E
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
- SCN · Thiocyanate ion · ion · chains E
- GOL · Glycerol · additive · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.83 | 0.87 | 32 | empty |
| 2 | 569 | 0.81 | 0.86 | 34 | empty |
| 3 | 863 | 0.72 | 0.76 | 65 | M88 |
| 4 | 219 | 0.68 | 0.85 | 24 | empty |
| 5 | 204 | 0.66 | 0.84 | 24 | empty |
Interfaces
8 interfaces between chains.
- A–B · 990 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 973 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 927 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 927 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 905 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6SSS · Crystal structure of Human Microsomal Glutathione S-Transferase 2 · the same entry in another collection · chain F against F, TM-score 1.00
- Q99735 · AlphaFold monomer V2.0 prediction for microsomal glutathione S-transferase 2 (Q99735) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q99735
- Elsewhere: RCSB PDB 6SSS · PDBe 6SSS · UniProt Q99735
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