MolNFT v1 · #13493 · protein
Horse liver alcohol dehydrogenase complexed to NADH and N-formyl piperdine
1LDE: “Horse liver alcohol dehydrogenase complexed to NADH and N-formyl piperdine”. X-ray diffraction, 3 ligands (NAD, FPI, ZN), 7 pockets (best druggability 0.77). MolNFT v1 #13493 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1LDE
- Type
- protein
- Length
- 1,496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Liver alcohol dehydrogenase
- EC
- 1.1.1.1
- UniProt
- P00327
- Ligands
- NAD, FPI, ZN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Liver alcohol dehydrogenase (EC 1.1.1.1) | protein | 374 | 30% helix, 26% strand | P00327 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- FPI · N-formylpiperidine · 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
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.77 | 0.84 | 67 | NAD, FPI |
| 2 | 563 | 0.75 | 0.82 | 68 | NAD, FPI |
| 3 | 564 | 0.73 | 0.80 | 64 | NAD, FPI |
| 4 | 506 | 0.72 | 0.81 | 62 | NAD, FPI |
| 5 | 406 | 0.67 | 0.80 | 48 | empty |
Interfaces
2 interfaces between chains.
- A–D · 1717 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 184 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1LDE · Horse liver alcohol dehydrogenase complexed to NADH and N-formyl piperdine · the same entry in another collection · chain B against B, TM-score 1.00
- P00327 · AlphaFold monomer V2.0 prediction for alcohol dehydrogenase E chain (P00327) · a predicted model of the same protein · chain D 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 P00327
- Elsewhere: RCSB PDB 1LDE · PDBe 1LDE · UniProt P00327
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