MolNFT v1 · #55028 · protein
Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (kce) from candidatus cloacamonas acidaminovorans (orthorombic form)
2Y7D: “Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (kce) from candidatus cloacamonas…”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.81). MolNFT v1 #55028 on GenesisL1: 3D structure, binding sites…
- PDB
- 2Y7D
- Type
- protein
- Length
- 1,094 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
- ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-keto-5-aminohexanoate cleavage enzyme | protein | 270 | 40% helix, 21% strand | B0VHH0 |
| B | 3-keto-5-aminohexanoate cleavage enzyme | protein | 277 | 40% helix, 20% strand | B0VHH0 |
| C | 3-keto-5-aminohexanoate cleavage enzyme | protein | 269 | 40% helix, 20% strand | B0VHH0 |
| D | 3-keto-5-aminohexanoate cleavage enzyme | protein | 278 | 40% helix, 20% strand | B0VHH0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.81 | 0.97 | 18 | empty |
| 2 | 936 | 0.75 | 0.78 | 131 | empty |
| 3 | 376 | 0.70 | 0.82 | 53 | empty |
| 4 | 356 | 0.67 | 0.81 | 55 | empty |
| 5 | 250 | 0.66 | 0.83 | 56 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1185 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1176 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 965 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 938 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2Y7D · Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from Candidatus… · 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 C against A, TM-score 0.98
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 2Y7D · PDBe 2Y7D · UniProt B0VHH0
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