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Activator of the 2-hydroxyisocaproyl-CoA dehydratase from clostridium difficile with bound adpnp
Analyse Activator of the 2-hydroxyisocaproyl-CoA dehydratase from clostridium difficile… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EHU
- Type
- protein
- Length
- 527 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activator of 2-hydroxyisocaproyl-CoA dehydratase
- UniProt
- Q5U925
- Ligands
- ANP, SF4, NA, MG
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activator of 2-hydroxyisocaproyl-CoA dehydratase | protein | 268 | 46% helix, 21% strand | Q5U925 |
| B | Activator of 2-hydroxyisocaproyl-CoA dehydratase | protein | 259 | 47% helix, 20% strand | Q5U925 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.65 | 0.84 | 35 | ANP, MG |
| 2 | 199 | 0.65 | 0.85 | 33 | ANP, MG, NA |
| 3 | 81 | 0.38 | 0.77 | 18 | SF4 |
| 4 | 88 | 0.34 | 0.74 | 18 | ACT |
| 5 | 108 | 0.34 | 0.72 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 559 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4EHU · Activator of the 2-Hydroxyisocaproyl-CoA Dehydratase from Clostridium difficile with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5U925 · AlphaFold monomer V2.0 prediction for 2-hydroxyisocaproyl-CoA dehydratase activator… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q5U925
- Elsewhere: RCSB PDB 4EHU · PDBe 4EHU · UniProt Q5U925
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