MolNFT v1 · #55031 · protein
Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (kce) from C. cloacamonas acidaminovorans in complex with the product acetoacetate
2Y7G: “Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (kce) from C. cloacamonas acidaminovorans in…”. X-ray diffraction, 3 ligands (AAE, ZN, MG), 6 pockets (best druggability 0.66). MolNFT v1 #55031 on GenesisL1: 3D…
- PDB
- 2Y7G
- Type
- protein
- Length
- 552 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-keto-5-aminohexanoate cleavage enzyme
- UniProt
- B0VHH0
- Ligands
- AAE, ZN, MG
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-keto-5-aminohexanoate cleavage enzyme | protein | 276 | 41% helix, 21% strand | B0VHH0 |
Ligands and binding sites
- AAE · Acetoacetic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.66 | 0.84 | 34 | ZN, AAE |
| 2 | 236 | 0.65 | 0.83 | 36 | ZN, AAE |
| 3 | 61 | 0.39 | 0.80 | 15 | empty |
| 4 | 134 | 0.37 | 0.72 | 25 | empty |
| 5 | 121 | 0.37 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2Y7G · Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from C.… · the same entry in another collection · chain A against A, TM-score 1.00
- B0VHH0 · AlphaFold monomer V2.0 prediction for 3-keto-5-aminohexanoate cleavage enzyme (B0VHH0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 B0VHH0
- Elsewhere: RCSB PDB 2Y7G · PDBe 2Y7G · UniProt B0VHH0
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