Research workbench
The crystal structure of the acdh domain of an alcohol dehydrogenase from vibrio parahaemolyticus to 2.25A
Analyse The crystal structure of the acdh domain of an alcohol dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MY7
- Type
- protein
- Length
- 1,651 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol DEHYDROGENASE/ACETALDEHYDE dehydrogenase
- UniProt
- Q87MW0
- Ligands
- CL
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alcohol DEHYDROGENASE/ACETALDEHYDE dehydrogenase | protein | 411 | 48% helix, 19% strand | Q87MW0 |
| B | Alcohol DEHYDROGENASE/ACETALDEHYDE dehydrogenase | protein | 415 | 46% helix, 18% strand | Q87MW0 |
| C | Alcohol DEHYDROGENASE/ACETALDEHYDE dehydrogenase | protein | 416 | 46% helix, 19% strand | Q87MW0 |
| D | Alcohol DEHYDROGENASE/ACETALDEHYDE dehydrogenase | protein | 409 | 46% helix, 20% strand | Q87MW0 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.77 | 0.81 | 89 | empty |
| 2 | 662 | 0.76 | 0.81 | 64 | empty |
| 3 | 574 | 0.72 | 0.80 | 70 | empty |
| 4 | 880 | 0.71 | 0.76 | 75 | empty |
| 5 | 258 | 0.54 | 0.77 | 33 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1151 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1121 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 180 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 86 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 3MY7 · The Crystal Structure of the ACDH domain of an Alcohol Dehydrogenase from Vibrio… · 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 Q87MW0
- Elsewhere: RCSB PDB 3MY7 · PDBe 3MY7 · UniProt Q87MW0
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