Research workbench
Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (kce)
Analyse Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (kce) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y7F
- Type
- protein
- Length
- 1,107 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-keto-5-aminohexanoate cleavage enzyme
- UniProt
- B0VHH0
- Ligands
- KMH, ZN, MG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | 3-keto-5-aminohexanoate cleavage enzyme | protein | 277 | 41% helix, 21% strand | B0VHH0 |
| B | 3-keto-5-aminohexanoate cleavage enzyme | protein | 276 | 41% helix, 21% strand | B0VHH0 |
Ligands and binding sites
- KMH · (5S)-5-amino-3-oxo-hexanoic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.82 | 0.98 | 19 | empty |
| 2 | 739 | 0.72 | 0.78 | 98 | empty |
| 3 | 790 | 0.69 | 0.75 | 92 | empty |
| 4 | 244 | 0.67 | 0.83 | 42 | empty |
| 5 | 224 | 0.65 | 0.83 | 44 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1171 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1167 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1025 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 941 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2Y7F · Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from C.… · the same entry in another collection · chain D against D, 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 B 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 2Y7F · PDBe 2Y7F · UniProt B0VHH0
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