MolNFT v1 · #10662 · protein

Crystal structure of levodione reductase

1IY8: “Crystal structure of levodione reductase”. X-ray diffraction, 1 ligand (NAD), 14 pockets (best druggability 0.86). MolNFT v1 #10662 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1IY8
Type: protein
Length: 2,064 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Levodione reductase
UniProt: Q9LBG2
Ligands: NAD
Pockets: 14 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Levodione reductase	protein	258	51% helix, 16% strand	Q9LBG2

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
MRD · (4R)-2-methylpentane-2,4-diol · additive · 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

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	673	0.86	0.91	53	empty
2	690	0.86	0.90	56	empty
3	1037	0.83	0.84	116	NAD, MRD
4	1068	0.83	0.84	117	NAD, MRD
5	1063	0.83	0.83	119	NAD, MRD

Interfaces

13 interfaces between chains.

A–C · 1608 Å² buried · 38 hydrogen bonds · protein-protein
B–D · 1604 Å² buried · 38 hydrogen bonds · protein-protein
E–G · 1604 Å² buried · 38 hydrogen bonds · protein-protein
F–H · 1598 Å² buried · 39 hydrogen bonds · protein-protein
B–C · 1431 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

1IY8 · Crystal Structure of Levodione Reductase · the same entry in another collection · chain H against H, TM-score 1.00
Q9LBG2 · AlphaFold monomer V2.0 prediction for levodione reductase (Q9LBG2) · a predicted model of the same protein · 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 Q9LBG2
Elsewhere: RCSB PDB 1IY8 · PDBe 1IY8 · UniProt Q9LBG2

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