MolNFT v1 · #137316 · protein
Cinnamyl alcohol dehydrogenases (SBCAD4) from sorghum bicolor (L.) moench
5VKT: “Cinnamyl alcohol dehydrogenases (SBCAD4) from sorghum bicolor (L.) moench”. X-ray diffraction, 3 ligands (NAP, MLT, ZN), 6 pockets (best druggability 0.69). MolNFT v1 #137316 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5VKT
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cinnamyl alcohol dehydrogenases (SBCAD4)
- EC
- 1.1.1.195
- UniProt
- C5XC49
- Ligands
- NAP, MLT, ZN
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cinnamyl alcohol dehydrogenases (SBCAD4) (EC 1.1.1.195) | protein | 353 | 28% helix, 27% strand | C5XC49 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- MLT · D-malate · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
- FMT · Formic acid · additive · chains A
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.69 | 0.77 | 62 | empty |
| 2 | 366 | 0.68 | 0.81 | 53 | FMT, NAP |
| 3 | 156 | 0.67 | 0.87 | 23 | empty |
| 4 | 400 | 0.61 | 0.77 | 47 | ACT |
| 5 | 99 | 0.38 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 333 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5VKT · Cinnamyl alcohol dehydrogenases (SbCAD4) from Sorghum bicolor (L.) Moench · 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
- Every structure of UniProt C5XC49
- Elsewhere: RCSB PDB 5VKT · PDBe 5VKT · UniProt C5XC49
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