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Ternary complex of saccharopine reductase from magnaporthe grisea, NADPH and saccharopine

Analyse Ternary complex of saccharopine reductase from magnaporthe grisea, NADPH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 826 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 825 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 821 Å² buried · 12 hydrogen bonds · protein-protein
F–G · 414 Å² 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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