Research workbench
Crystal structure of 4-hydroxybutyryl-CoA dehydratase from clostridium aminobutyricum: radical catalysis involving a [4FE-4S] cluster and flavin
Analyse Crystal structure of 4-hydroxybutyryl-CoA dehydratase from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U8V
- Type
- protein
- Length
- 1,960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyrate metabolism DEHYDRATASE/ISOMERASE
- EC
- 4.2.-.-, 5.3.3.3
- UniProt
- P55792
- Ligands
- SF4, FAD
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Gamma-aminobutyrate metabolism DEHYDRATASE/ISOMERASE (EC 4.2.-.-, 5.3.3.3) | protein | 490 | 53% helix, 13% strand | P55792 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.84 | 0.86 | 80 | empty |
| 2 | 901 | 0.82 | 0.84 | 97 | SF4, FAD |
| 3 | 920 | 0.82 | 0.84 | 104 | SF4, FAD |
| 4 | 876 | 0.82 | 0.84 | 92 | SF4, FAD |
| 5 | 918 | 0.82 | 0.83 | 99 | SF4, FAD |
Interfaces
6 interfaces between chains.
- A–B · 3713 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 3696 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 2582 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2571 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 59 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1U8V · Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum… · the same entry in another collection · chain A against A, TM-score 1.00
- P55792 · AlphaFold monomer V2.0 prediction for 4-hydroxybutyryl-CoA… · a predicted model of the same protein · chain A 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 P55792
- Elsewhere: RCSB PDB 1U8V · PDBe 1U8V · UniProt P55792
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