MolNFT v1 · #147485 · protein
Streptomyces bingchenggensis aldolase-dehydratase in covalent complex with dienone product.
6EEJ · Acetoacetate decarboxylase: “Streptomyces bingchenggensis aldolase-dehydratase in covalent complex with dienone product.”. X-ray diffraction, 2 ligands (J6S, K), 10 pockets (best druggability 0.83). MolNFT v1 #147485 on GenesisL1…
- PDB
- 6EEJ
- Type
- protein
- Length
- 1,052 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoacetate decarboxylase
- UniProt
- D7C0E5
- Ligands
- J6S, K
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Acetoacetate decarboxylase | protein | 264 | 12% helix, 50% strand | D7C0E5 |
| B | Acetoacetate decarboxylase | protein | 260 | 10% helix, 51% strand | D7C0E5 |
Ligands and binding sites
- J6S · (3E,5E)-6-(4-nitrophenyl)-2-oxohexa-3,5-dienoic acid · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.83 | 0.84 | 145 | empty |
| 2 | 274 | 0.75 | 0.87 | 37 | J6S |
| 3 | 292 | 0.75 | 0.87 | 39 | J6S |
| 4 | 268 | 0.74 | 0.87 | 39 | J6S |
| 5 | 421 | 0.68 | 0.79 | 41 | J6S |
Interfaces
6 interfaces between chains.
- A–D · 2705 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2694 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1677 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1671 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 272 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6EEJ · Streptomyces bingchenggensis Aldolase-Dehydratase in covalent complex with die product. · 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 6EEJ · PDBe 6EEJ · UniProt D7C0E5
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