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Structural basis for stereo selectivity in the (R)- and (S)-hydroxypropylethane thiosulfonate dehydrogenases
Analyse Structural basis for stereo selectivity in the (R)- and (S)-hydroxypropylethane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CFC
- Type
- protein
- Length
- 1,000 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-(R)-hydroxypropyl-com dehydrogenase
- EC
- 1.1.1.268
- UniProt
- Q56840
- Ligands
- NAD, KPC
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-(R)-hydroxypropyl-com dehydrogenase (EC 1.1.1.268) | protein | 250 | 51% helix, 16% strand | Q56840 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- KPC · (2-[2-ketopropylthio]ethanesulfonate · ligand · 4 copies · chains A, B, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.85 | 0.87 | 58 | empty |
| 2 | 290 | 0.76 | 0.88 | 42 | NAD, KPC |
| 3 | 429 | 0.76 | 0.85 | 45 | NAD, KPC |
| 4 | 330 | 0.73 | 0.85 | 46 | NAD, KPC |
| 5 | 420 | 0.71 | 0.82 | 50 | NAD, KPC |
Interfaces
6 interfaces between chains.
- A–B · 1653 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1639 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1344 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1341 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 380 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2CFC · structural basis for stereo selectivity in the (R)- and (S)- hydroxypropylethane… · the same entry in another collection · chain A against A, TM-score 1.00
- Q56840 · AlphaFold monomer V2.0 prediction for 2-(R)-hydroxypropyl-com dehydrogenase (Q56840) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q56840
- Elsewhere: RCSB PDB 2CFC · PDBe 2CFC · UniProt Q56840
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