MolNFT v1 · #83955 · protein

Crystal structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with NAD+

3WYE · Diacetyl reductase [(S)-acetoin FORMING],L-2,3-butanediol…: “Crystal structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with NAD+”. X-ray diffraction, 1 ligand (NAD), 3 pockets (best druggability 0.72).…

PDB: 3WYE
Type: protein
Length: 494 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diacetyl reductase [(S)-acetoin FORMING],L-2,3-butanediol DEHYDROGENASE,DIACETYL…
EC: 1.1.1.304, 1.1.1.76
UniProt: Q48436, Q9ZNN8
Ligands: NAD
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diacetyl reductase [(S)-acetoin FORMING],L-2,3-butanediol DEHYDROGENASE,DIACETYL reductase [(S)-acetoin FORMING],L-2,3- butanediol DEHYDROGENASE,DIACETYL reductase [(S)-acetoin FORMING],L- 2,3-butanediol DEHYDROGENASE,DIACETYL reductase [(S)-acetoin forming] (EC 1.1.1.304, 1.1.1.76)	protein	255	53% helix, 16% strand	Q48436, Q9ZNN8
B	Diacetyl reductase [(S)-acetoin FORMING],L-2,3-butanediol DEHYDROGENASE,DIACETYL reductase [(S)-acetoin FORMING],L-2,3- butanediol DEHYDROGENASE,DIACETYL reductase [(S)-acetoin FORMING],L- 2,3-butanediol DEHYDROGENASE,DIACETYL reductase [(S)-acetoin forming] (EC 1.1.1.304, 1.1.1.76)	protein	239	51% helix, 17% strand	Q48436, Q9ZNN8

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	312	0.72	0.85	46	NAD
2	326	0.70	0.83	43	NAD
3	145	0.41	0.74	25	empty

Interfaces

1 interface between chains.

A–B · 1625 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3WYE · Crystal Structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
Q48436 · AlphaFold monomer V2.0 prediction for diacetyl reductase [(S)-acetoin forming] (Q48436) · a predicted model of the same protein · chain B against A, TM-score 0.99
Q9ZNN8 · AlphaFold monomer V2.0 prediction for L-2,3-butanediol dehydrogenase (Q9ZNN8) · a predicted model of the same protein · chain A 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 Q48436
Every structure of UniProt Q9ZNN8
Elsewhere: RCSB PDB 3WYE · PDBe 3WYE · UniProt Q48436 · UniProt Q9ZNN8

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