MolNFT v1 · #112132 · protein
Streptomyces bingchenggensis aldolase-dehydratase in schiff base complex with pyruvate
4ZBT · Acetoacetate decarboxylase: “Streptomyces bingchenggensis aldolase-dehydratase in schiff base complex with pyruvate”. X-ray diffraction, 1 ligand (PYR), 9 pockets (best druggability 0.83). MolNFT v1 #112132 on GenesisL1: 3D…
- PDB
- 4ZBT
- Type
- protein
- Length
- 1,028 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoacetate decarboxylase
- UniProt
- D7C0E5
- Ligands
- PYR
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetoacetate decarboxylase | protein | 260 | 11% helix, 48% strand | D7C0E5 |
| B | Acetoacetate decarboxylase | protein | 254 | 10% helix, 51% strand | D7C0E5 |
| C | Acetoacetate decarboxylase | protein | 252 | 10% helix, 51% strand | D7C0E5 |
| D | Acetoacetate decarboxylase | protein | 262 | 11% helix, 49% strand | D7C0E5 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 6 copies · chains A, B, C, D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, C, D, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.83 | 0.84 | 159 | empty |
| 2 | 282 | 0.72 | 0.85 | 42 | PYR |
| 3 | 285 | 0.68 | 0.83 | 42 | PYR |
| 4 | 218 | 0.64 | 0.83 | 33 | empty |
| 5 | 339 | 0.63 | 0.78 | 40 | PYR |
Interfaces
6 interfaces between chains.
- A–C · 2702 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 2700 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1681 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1678 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 276 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4ZBT · Streptomyces bingchenggensis aldolase-dehydratase in Schiff base complex with pyruvate · 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 D7C0E5
- Elsewhere: RCSB PDB 4ZBT · PDBe 4ZBT · UniProt D7C0E5
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