MolNFT v1 · #123176 · protein
Crystal structure of liuc in complex with coenzyme a and malonic acid
5JBX · 3-hydroxybutyryl-CoA dehydratase: “Crystal structure of liuc in complex with coenzyme a and malonic acid”. X-ray diffraction, 1 ligand (COA), 7 pockets (best druggability 0.87). MolNFT v1 #123176 on GenesisL1: 3D structure, binding…
- PDB
- 5JBX
- Type
- protein
- Length
- 780 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxybutyryl-CoA dehydratase
- EC
- 4.2.1.55
- UniProt
- Q1D5Y4
- Ligands
- COA
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) | protein | 258 | 52% helix, 16% strand | Q1D5Y4 |
| B, C | 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) | protein | 261 | 51% helix, 17% strand | Q1D5Y4 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, C, B
- MLI · Malonate ion · additive · 4 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.87 | 0.92 | 79 | empty |
| 2 | 155 | 0.71 | 0.90 | 23 | empty |
| 3 | 359 | 0.69 | 0.82 | 48 | empty |
| 4 | 257 | 0.67 | 0.83 | 42 | COA, MLI |
| 5 | 258 | 0.64 | 0.81 | 41 | COA, MLI |
Interfaces
3 interfaces between chains.
- A–B · 2018 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1997 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1712 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5JBX · Crystal structure of LiuC in complex with coenzyme A and malonic acid · the same entry in another collection · chain B against B, 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 Q1D5Y4
- Elsewhere: RCSB PDB 5JBX · PDBe 5JBX · UniProt Q1D5Y4
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