MolNFT v1 · #13508 · protein
Horse liver alcohol dehydrogenase complexed to NADH and cyclohexyl formamide (cxf)
1LDY: “Horse liver alcohol dehydrogenase complexed to NADH and cyclohexyl formamide (cxf)”. X-ray diffraction, 3 ligands (NAD, CXF, ZN), 9 pockets (best druggability 0.77). MolNFT v1 #13508 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1LDY
- Type
- protein
- Length
- 1,496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase
- EC
- 1.1.1.1
- UniProt
- P00327
- Ligands
- NAD, CXF, ZN
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 374 | 31% helix, 26% strand | P00327 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- CXF · Cyclohexylformamide · 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
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.77 | 0.84 | 61 | NAD, CXF |
| 2 | 549 | 0.77 | 0.83 | 69 | NAD, CXF |
| 3 | 547 | 0.76 | 0.83 | 68 | NAD, CXF |
| 4 | 642 | 0.76 | 0.82 | 76 | NAD, CXF |
| 5 | 363 | 0.67 | 0.81 | 49 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1767 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1765 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 183 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 181 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 61 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1LDY · Horse liver alcohol dehydrogenase complexed to NADH and cyclohexyl formamide (cxf) · the same entry in another collection · chain D against D, TM-score 1.00
- P00327 · AlphaFold monomer V2.0 prediction for alcohol dehydrogenase E chain (P00327) · a predicted model of the same protein · chain B 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 1LDY · PDBe 1LDY · UniProt P00327
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