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Crystal and solution structures of the bifunctional enzyme (ALDOLASE/ALDEHYDE dehydrogenase) from thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site
Analyse Crystal and solution structures of the bifunctional enzyme (ALDOLASE/ALDEHYDE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LRT
- Type
- protein
- Length
- 1,257 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-2-oxovalerate aldolase; Acetaldehyde dehydrogenase
- EC
- 4.1.3.39, 1.2.1.10
- UniProt
- D1A3K8, D1A3K7
- Ligands
- PYR, COA, NA, MG, SO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) | protein | 334 | 49% helix, 16% strand | D1A3K8 |
| B | Acetaldehyde dehydrogenase (EC 1.2.1.10) | protein | 295 | 41% helix, 24% strand | D1A3K7 |
| C | 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) | protein | 335 | 50% helix, 16% strand | D1A3K8 |
| D | Acetaldehyde dehydrogenase (EC 1.2.1.10) | protein | 293 | 41% helix, 23% strand | D1A3K7 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, C
- COA · Coenzyme A · ligand · 2 copies · chains B, D
- NA · Sodium ion · metal · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.82 | 0.98 | 23 | empty |
| 2 | 78 | 0.74 | 0.98 | 22 | empty |
| 3 | 55 | 0.73 | 0.99 | 17 | empty |
| 4 | 55 | 0.71 | 0.98 | 18 | empty |
| 5 | 358 | 0.70 | 0.82 | 37 | NA, COA |
Interfaces
3 interfaces between chains.
- A–C · 1755 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1712 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1634 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4LRT · Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde… · the same entry in another collection · 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 D1A3K8
- Every structure of UniProt D1A3K7
- Elsewhere: RCSB PDB 4LRT · PDBe 4LRT · UniProt D1A3K8 · UniProt D1A3K7
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