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Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (kce) from candidatus cloacamonas acidaminovorans (tetragonal form)
Analyse Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (kce) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y7E
- 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
- ZN, MG
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-keto-5-aminohexanoate cleavage enzyme | protein | 274 | 41% helix, 21% strand | B0VHH0 |
| B | 3-keto-5-aminohexanoate cleavage enzyme | protein | 278 | 41% helix, 21% strand | B0VHH0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- FMT · Formic acid · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.64 | 0.83 | 33 | ZN, FMT |
| 2 | 269 | 0.64 | 0.82 | 46 | ZN, FMT |
| 3 | 232 | 0.53 | 0.76 | 38 | empty |
| 4 | 180 | 0.50 | 0.77 | 23 | empty |
| 5 | 54 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 938 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2Y7E · Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from Candidatus… · 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 2Y7E · PDBe 2Y7E · UniProt B0VHH0
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