MolNFT v1 · #119790 · protein
Imine reductase from aspergillus oryzae in complex with NADP(H) and (R)-rasagiline
5G6S: “Imine reductase from aspergillus oryzae in complex with NADP(H) and (R)-rasagiline”. X-ray diffraction, 2 ligands (NDP, RAU), 17 pockets (best druggability 0.78). MolNFT v1 #119790 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5G6S
- Type
- protein
- Length
- 2,309 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imine reductase
- EC
- 1.5.1.48
- UniProt
- Q2TW47
- Ligands
- NDP, RAU
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, G, H | Imine reductase (EC 1.5.1.48) | protein | 289 | 56% helix, 14% strand | Q2TW47 |
| C, D, E | Imine reductase (EC 1.5.1.48) | protein | 288 | 56% helix, 14% strand | Q2TW47 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, G, B, C, D, F, E, H
- RAU · Rasagiline · ligand · 8 copies · chains A, G, B, C, D, F, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.78 | 0.88 | 41 | NDP, RAU |
| 2 | 345 | 0.77 | 0.88 | 43 | NDP, RAU |
| 3 | 357 | 0.77 | 0.87 | 44 | NDP, RAU |
| 4 | 347 | 0.77 | 0.87 | 43 | NDP, RAU |
| 5 | 346 | 0.77 | 0.87 | 41 | NDP, RAU |
Interfaces
10 interfaces between chains.
- E–H · 4412 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 4412 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 4408 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 4400 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 337 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5G6S · Imine reductase from Aspergillus oryzae in complex with NADP(H) and (R)-rasagiline · the same entry in another collection · chain H against H, TM-score 1.00
- Q2TW47 · AlphaFold monomer V2.0 prediction for NADPH-dependent reductive aminase (Q2TW47) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q2TW47
- Elsewhere: RCSB PDB 5G6S · PDBe 5G6S · UniProt Q2TW47
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