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Crystal structure of malus domestica double bond reductase (mddbr) ternary complex

Analyse Crystal structure of malus domestica double bond reductase (mddbr) ternary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YUX
Type: protein
Length: 342 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Double bond reductase
Ligands: NAP, FER, NA
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Double bond reductase	protein	342	32% helix, 28% strand	—

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
FER · 3-(4-hydroxy-3-methoxyphenyl)-2-propenoic acid · ligand · chains A
NA · Sodium ion · metal · 2 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	517	0.77	0.84	58	NAP, EDO, FER, NA
2	53	0.29	0.75	10	MPD

Compared structures

6YUX · Crystal structure of Malus domestica Double Bond Reductase (MdDBR) ternary complex · the same entry in another collection · 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
Elsewhere: RCSB PDB 6YUX · PDBe 6YUX

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