Research workbench
D275P mutant of alcohol dehydrogenase from protozoa entamoeba histolytica
Analyse D275P mutant of alcohol dehydrogenase from protozoa entamoeba histolytica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OUI
- Type
- protein
- Length
- 1,440 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
- P35630
- Ligands
- ZN, NO3, CL
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADP-dependent alcohol dehydrogenase (EC 1.1.1.2) | protein | 360 | 30% helix, 26% strand | P35630 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 4 copies · chains A, B, D
- CL · Chloride ion · ion · chains D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, B, C
- CAC · Cacodylate ion · additive · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · chains C
- PG4 · Tetraethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.82 | 0.83 | 121 | EDO, PGE |
| 2 | 349 | 0.70 | 0.83 | 45 | CAC |
| 3 | 417 | 0.68 | 0.80 | 52 | CAC |
| 4 | 438 | 0.68 | 0.80 | 53 | NO3, CAC, EDO |
| 5 | 385 | 0.68 | 0.81 | 37 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2011 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1986 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 850 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 839 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 701 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2OUI · D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica · the same entry in another collection · chain D against D, TM-score 1.00
- P35630 · AlphaFold monomer V2.0 prediction for NADP-dependent isopropanol dehydrogenase (P35630) · 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 P35630
- Elsewhere: RCSB PDB 2OUI · PDBe 2OUI · UniProt P35630
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