MolNFT v1 · #78215 · protein
Crystal structure of furx NADH complex 1
3S2E · Zinc-containing alcohol dehydrogenase superfamily: “Crystal structure of furx NADH complex 1”. X-ray diffraction, 3 ligands (NAD, ZN, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #78215 on GenesisL1: 3D structure, binding…
- PDB
- 3S2E
- 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
- NAD, ZN, SO4
- Pockets
- 20 · best druggability 0.81
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
- NAD · Nicotinamide-adenine-dinucleotide · 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 · 13 copies · chains A, B, C, D, E, G, H
- GOL · Glycerol · additive · 11 copies · chains A, G, B, H, C, E, D, F
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 | 683 | 0.81 | 0.85 | 106 | GOL, SO4 |
| 2 | 840 | 0.80 | 0.83 | 117 | GOL, SO4 |
| 3 | 343 | 0.78 | 0.88 | 53 | NAD |
| 4 | 563 | 0.78 | 0.85 | 70 | GOL, SO4 |
| 5 | 888 | 0.77 | 0.80 | 104 | empty |
Interfaces
14 interfaces between chains.
- B–H · 1761 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1753 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 1740 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1721 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 583 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3S2E · Crystal Structure of FurX NADH Complex 1 · 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 3S2E · PDBe 3S2E · UniProt Q46UZ9
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