MolNFT v1 · #171145 · protein
Crystal structure of malus domestica double bond reductase (mddbr) ternary complex
6YUX: “Crystal structure of malus domestica double bond reductase (mddbr) ternary complex”. X-ray diffraction, 3 ligands (NAP, FER, NA), 2 pockets (best druggability 0.77). MolNFT v1 #171145 on GenesisL1: 3D structure, binding sites and…
- 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.
| Volume (ų) | 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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