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Crystal structure of glutathione S-transferase from sinorhizobium meliloti 1021, nysgrc target 021389
Analyse Crystal structure of glutathione S-transferase from sinorhizobium meliloti… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MDC
- Type
- protein
- Length
- 930 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glutathione S-transferase
- EC
- 2.5.1.18
- UniProt
- Q92SP3
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glutathione S-transferase (EC 2.5.1.18) | protein | 231 | 59% helix, 8% strand | Q92SP3 |
| B, C, D | Putative glutathione S-transferase (EC 2.5.1.18) | protein | 233 | 56% helix, 8% strand | Q92SP3 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.78 | 0.80 | 81 | empty |
| 2 | 1017 | 0.78 | 0.79 | 78 | empty |
| 3 | 414 | 0.63 | 0.77 | 48 | GOL |
| 4 | 145 | 0.45 | 0.76 | 26 | empty |
| 5 | 134 | 0.43 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1099 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1072 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 403 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4MDC · Crystal structure of glutathione S-transferase from Sinorhizobium meliloti 1021, NYSGRC… · 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 Q92SP3
- Elsewhere: RCSB PDB 4MDC · PDBe 4MDC · UniProt Q92SP3
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