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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
- 4LRS
- Type
- protein
- Length
- 634 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-2-oxovalerate aldolase; Acetaldehyde dehydrogenase; Symmetric aldolase…
- EC
- 4.1.3.39, 1.2.1.10
- UniProt
- D1A3K8, D1A3K7
- Ligands
- PYR, NAD, FOR, MG, CL, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) | protein | 337 | 50% helix, 16% strand | D1A3K8 |
| B | Acetaldehyde dehydrogenase (EC 1.2.1.10) | protein | 294 | 39% helix, 24% strand | D1A3K7 |
| N | Symmetric aldolase, C-terminal disordered residues | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains B
- FOR · Formyl group · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, N
- GOL · Glycerol · additive · 6 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.73 | 0.99 | 17 | FOR |
| 2 | 202 | 0.72 | 0.89 | 48 | empty |
| 3 | 335 | 0.67 | 0.81 | 67 | NAD, PEG |
| 4 | 266 | 0.52 | 0.75 | 34 | empty |
| 5 | 105 | 0.40 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1594 Ų buried · 29 hydrogen bonds · protein-protein
- B–N · 66 Ų buried · 0 hydrogen bonds · protein-protein
- A–N · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4LRS · 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 4LRS · PDBe 4LRS · UniProt D1A3K8 · UniProt D1A3K7
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