Research workbench
A single amino acid substitution in the clostridium beijerinckii alcohol dehydrogenase is critical for thermostabilization
Analyse A single amino acid substitution in the clostridium beijerinckii alcohol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B83
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent alcohol dehydrogenase
- EC
- 1.1.1.2
- UniProt
- P25984
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADP-dependent alcohol dehydrogenase (EC 1.1.1.2) | protein | 351 | 32% helix, 25% strand | P25984 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.81 | 0.82 | 100 | empty |
| 2 | 1119 | 0.81 | 0.82 | 107 | empty |
| 3 | 416 | 0.74 | 0.84 | 50 | empty |
| 4 | 356 | 0.73 | 0.85 | 42 | empty |
| 5 | 363 | 0.73 | 0.84 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1772 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1764 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1075 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1038 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 776 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2B83 · A single amino acid substitution in the Clostridium beijerinckii alcohol dehydrogenase is… · the same entry in another collection · chain D against D, TM-score 1.00
- P25984 · AlphaFold monomer V2.0 prediction for NADP-dependent isopropanol dehydrogenase (P25984) · 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 P25984
- Elsewhere: RCSB PDB 2B83 · PDBe 2B83 · UniProt P25984
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