Research workbench
S-enantioselective imine reductase from mycobacterium smegmatis
Analyse S-enantioselective imine reductase from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SMT
- Type
- protein
- Length
- 1,432 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase, NAD-binding
- UniProt
- A0R5X0
- Ligands
- NDP, 2EH
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | 6-phosphogluconate dehydrogenase, NAD-binding | protein | 286 | 59% helix, 15% strand | A0R5X0 |
| B | 6-phosphogluconate dehydrogenase, NAD-binding | protein | 289 | 58% helix, 14% strand | A0R5X0 |
| C | 6-phosphogluconate dehydrogenase, NAD-binding | protein | 285 | 57% helix, 15% strand | A0R5X0 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 5 copies · chains A, B, C, D, E
- 2EH · (2S)-2-ethylhexan-1-ol · ligand · 5 copies · chains A, B, C, D, E
- FMT · Formic acid · additive · 12 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, E
- GOL · Glycerol · additive · 3 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.80 | 0.86 | 50 | NDP, FMT, 2EH |
| 2 | 515 | 0.79 | 0.86 | 52 | GOL, NDP, 2EH |
| 3 | 520 | 0.79 | 0.86 | 53 | NDP, FMT, 2EH |
| 4 | 595 | 0.79 | 0.84 | 57 | NDP, FMT, 2EH |
| 5 | 518 | 0.59 | 0.73 | 42 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4266 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 4226 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 348 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 62 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SMT · S-enantioselective imine reductase from Mycobacterium smegmatis · 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 A0R5X0
- Elsewhere: RCSB PDB 6SMT · PDBe 6SMT · UniProt A0R5X0
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