MolNFT v1 · #179658 · protein
Symmetry in yeast alcohol dehydrogenase 1 -closed form with NAD+ and trifluoroethanol
7KCB · ADH1 isoform 1: “Symmetry in yeast alcohol dehydrogenase 1 -closed form with NAD+ and trifluoroethanol”. Electron microscopy, 2 ligands (NAD, ZN), 15 pockets (best druggability 0.77). MolNFT v1 #179658 on GenesisL1: 3D structure…
- PDB
- 7KCB
- Type
- protein
- Length
- 1,388 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADH1 isoform 1
- UniProt
- A0A6A5Q6H9
- Ligands
- NAD, ZN
- Pockets
- 15 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ADH1 isoform 1 | protein | 347 | 27% helix, 29% strand | A0A6A5Q6H9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- ETF · Trifluoroethanol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.77 | 0.82 | 99 | empty |
| 2 | 280 | 0.75 | 0.88 | 46 | NAD, ETF |
| 3 | 301 | 0.75 | 0.87 | 46 | NAD, ETF |
| 4 | 274 | 0.74 | 0.87 | 45 | NAD, ETF |
| 5 | 299 | 0.74 | 0.86 | 48 | NAD, ETF |
Interfaces
6 interfaces between chains.
- A–D · 1601 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1601 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 642 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 642 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7KCB · Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NAD+ and Trifluoroethanol · 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 A0A6A5Q6H9
- Elsewhere: RCSB PDB 7KCB · PDBe 7KCB · UniProt A0A6A5Q6H9
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