Research workbench
Horse liver alcohol dehydrogenase complexed with NADH and N- benzyformamide
Analyse Horse liver alcohol dehydrogenase complexed with NADH and N- benzyformamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VL0
- 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, BNF, 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 E chain (EC 1.1.1.1) | protein | 374 | 31% helix, 26% strand | P00327 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- BNF · N-benzylformamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains B, C
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 | 528 | 0.77 | 0.84 | 64 | NAI, BNF |
| 2 | 652 | 0.76 | 0.82 | 74 | NAI, BNF |
| 3 | 568 | 0.76 | 0.83 | 68 | NAI, BNF |
| 4 | 584 | 0.76 | 0.83 | 73 | NAI, BNF |
| 5 | 424 | 0.68 | 0.80 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1739 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1735 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 242 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 173 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VL0 · horse liver alcohol dehydrogenase complexed with NADH and N-benzyformamide · 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 5VL0 · PDBe 5VL0 · UniProt P00327
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