Research workbench
Horse liver alcohol dehydrogenase complexed with NADH and R- N-1-methylhexylformamide
Analyse Horse liver alcohol dehydrogenase complexed with NADH and R… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P1R
- Type
- protein
- Length
- 1,496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase E chain
- EC
- 1.1.1.1
- UniProt
- P00327
- Ligands
- NAI, NMH, ZN
- Pockets
- 10 · 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 | Alcohol dehydrogenase E chain (EC 1.1.1.1) | protein | 374 | 30% helix, 26% strand | P00327 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NMH · (R)-N-(1-methyl-hexyl)-formamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.77 | 0.84 | 64 | NAI, NMH |
| 2 | 1063 | 0.77 | 0.79 | 111 | NAI, NMH |
| 3 | 573 | 0.76 | 0.83 | 73 | NAI, NMH |
| 4 | 544 | 0.76 | 0.83 | 66 | NAI, NMH |
| 5 | 419 | 0.68 | 0.80 | 48 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1708 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1697 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 214 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 163 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1P1R · Horse liver alcohol dehydrogenase complexed with NADH and R-N-1-methylhexylformamide · 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 C 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 1P1R · PDBe 1P1R · UniProt P00327
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