Research workbench
Symmetry in yeast alcohol dehydrogenase 1 -closed form with NADH
Analyse Symmetry in yeast alcohol dehydrogenase 1 -closed form with NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KC2
- 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
- 19 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 347 | 28% helix, 27% strand | S5RZC2 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.76 | 0.87 | 46 | NAD |
| 2 | 334 | 0.76 | 0.87 | 49 | NAD |
| 3 | 338 | 0.75 | 0.86 | 53 | ZN, NAD |
| 4 | 327 | 0.74 | 0.86 | 48 | NAD |
| 5 | 275 | 0.70 | 0.85 | 48 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1641 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1632 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 635 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 635 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 508 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7KC2 · Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed 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 7KC2 · PDBe 7KC2 · UniProt S5RZC2
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