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Crystal structure of furx NADH:FURFURAL
Analyse Crystal structure of furx NADH:FURFURAL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S2F
- Type
- protein
- Length
- 2,720 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc-containing alcohol dehydrogenase superfamily
- UniProt
- Q46UZ9
- Ligands
- ISP, NAD, FU2, ZN, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Zinc-containing alcohol dehydrogenase superfamily | protein | 340 | 30% helix, 29% strand | Q46UZ9 |
Ligands and binding sites
- ISP · Phosphorylisopropane · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains C, E, D, F, A, G, B, H
- FU2 · Furfural · ligand · 4 copies · chains C, E, D, F, A, G, B, H
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 14 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
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.82 | 0.83 | 160 | ISP, SO4 |
| 2 | 518 | 0.78 | 0.85 | 72 | NAD, FU2 |
| 3 | 954 | 0.78 | 0.80 | 100 | empty |
| 4 | 557 | 0.77 | 0.84 | 81 | ISP, SO4 |
| 5 | 496 | 0.77 | 0.84 | 69 | NAD, FU2 |
Interfaces
14 interfaces between chains.
- A–G · 1758 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1747 Ų buried · 22 hydrogen bonds · protein-protein
- B–H · 1745 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 1742 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 578 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3S2F · Crystal Structure of FurX NADH:Furfural · 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 Q46UZ9
- Elsewhere: RCSB PDB 3S2F · PDBe 3S2F · UniProt Q46UZ9
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