MolNFT v1 · #5029 · protein
Ternary complex of saccharopine reductase from magnaporthe grisea, NADPH and saccharopine
1E5Q · Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]: “Ternary complex of saccharopine reductase from magnaporthe grisea, NADPH and saccharopine”. X-ray diffraction, 2 ligands (NDP, SHR), 20 pockets (best druggability 0.78).…
- PDB
- 1E5Q
- Type
- protein
- Length
- 3,592 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
- EC
- 1.5.1.10
- UniProt
- Q9P4R4
- Ligands
- NDP, SHR
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] (EC 1.5.1.10) | protein | 449 | 40% helix, 23% strand | Q9P4R4 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SHR · N-(5-amino-5-carboxypentyl)glutamic 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.78 | 0.83 | 68 | NDP, SHR |
| 2 | 838 | 0.78 | 0.81 | 89 | NDP, SHR |
| 3 | 692 | 0.78 | 0.83 | 68 | NDP, SHR |
| 4 | 659 | 0.78 | 0.83 | 67 | NDP, SHR |
| 5 | 666 | 0.78 | 0.83 | 64 | NDP, SHR |
Interfaces
8 interfaces between chains.
- A–B · 831 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 826 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 825 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 821 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 414 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1E5Q · Ternary complex of saccharopine reductase from Magnaporthe grisea, NADPH and saccharopine · the same entry in another collection · chain E against E, TM-score 1.00
- Q9P4R4 · AlphaFold monomer V2.0 prediction for saccharopine dehydrogenase [NADP(+)… · a predicted model of the same protein · chain A 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 Q9P4R4
- Elsewhere: RCSB PDB 1E5Q · PDBe 1E5Q · UniProt Q9P4R4
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