MolNFT v1 · #179921 · protein
Symmetry in yeast alcohol dehydrogenase 1 - open form with NADH
7KJY: “Symmetry in yeast alcohol dehydrogenase 1 - open form with NADH”. Electron microscopy, 2 ligands (NAD, ZN), 20 pockets (best druggability 0.75). MolNFT v1 #179921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KJY
- Type
- protein
- Length
- 1,388 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase
- EC
- 1.1.1.1
- UniProt
- S5RZC2
- Ligands
- NAD, ZN
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 347 | 29% helix, 27% strand | S5RZC2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.75 | 0.81 | 111 | empty |
| 2 | 114 | 0.74 | 0.95 | 24 | empty |
| 3 | 397 | 0.73 | 0.84 | 51 | NAD |
| 4 | 407 | 0.73 | 0.83 | 53 | NAD |
| 5 | 111 | 0.73 | 0.94 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1631 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1608 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 901 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 886 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 519 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7KJY · Symmetry in Yeast Alcohol Dehydrogenase 1 - Open Form with NADH · 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 S5RZC2
- Elsewhere: RCSB PDB 7KJY · PDBe 7KJY · UniProt S5RZC2
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