Research workbench
Crystal structure of 3-hydroxybutyryl-CoA dehydrogenase from escherichia COLI K12 substr. MG1655
Analyse Crystal structure of 3-hydroxybutyryl-CoA dehydrogenase from escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MOG
- Type
- protein
- Length
- 1,412 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 3-hydroxybutyryl-CoA dehydrogenase
- EC
- 1.1.1.157
- UniProt
- P76083
- Ligands
- CL
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) | protein | 470 | 49% helix, 14% strand | P76083 |
| C | Probable 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) | protein | 472 | 50% helix, 14% strand | P76083 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.81 | 0.96 | 35 | empty |
| 2 | 915 | 0.78 | 0.80 | 102 | CL |
| 3 | 392 | 0.76 | 0.86 | 50 | empty |
| 4 | 695 | 0.70 | 0.77 | 75 | CL |
| 5 | 388 | 0.65 | 0.79 | 42 | CL |
Interfaces
3 interfaces between chains.
- A–C · 1212 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1173 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1165 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3MOG · Crystal structure of 3-hydroxybutyryl-CoA dehydrogenase from Escherichia coli K12 substr.… · the same entry in another collection · chain A against A, TM-score 1.00
- P76083 · AlphaFold monomer V2.0 prediction for 3-hydroxyadipyl-CoA dehydrogenase (P76083) · a predicted model of the same protein · chain C 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 P76083
- Elsewhere: RCSB PDB 3MOG · PDBe 3MOG · UniProt P76083
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