MolNFT v1 · #40853 · protein
Structural of abdh, a beta-diketone hydrolase from the cyanobacterium anabaena sp. pcc 7120 bound to (S)-3- oxocyclohexyl acetic acid
2J5S: “Structural of abdh, a beta-diketone hydrolase from the cyanobacterium anabaena sp. pcc 7120 bound to (S)-3…”. X-ray diffraction, 2 ligands (KTA, NI), 9 pockets (best druggability 0.74). MolNFT v1 #40853 on GenesisL1: 3D structure…
- PDB
- 2J5S
- Type
- protein
- Length
- 498 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-diketone hydrolase
- EC
- 3.7.1.7
- UniProt
- Q8YNV6
- Ligands
- KTA, NI
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-diketone hydrolase (EC 3.7.1.7) | protein | 250 | 51% helix, 18% strand | Q8YNV6 |
| B | Beta-diketone hydrolase (EC 3.7.1.7) | protein | 248 | 53% helix, 18% strand | Q8YNV6 |
Ligands and binding sites
- KTA · (S)-cyclohexanone-2-acetate · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.74 | 0.84 | 53 | empty |
| 2 | 125 | 0.68 | 0.90 | 35 | KTA |
| 3 | 144 | 0.68 | 0.88 | 29 | KTA |
| 4 | 123 | 0.42 | 0.76 | 19 | empty |
| 5 | 110 | 0.41 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1208 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2J5S · Structural of ABDH, a beta-diketone hydrolase from the Cyanobacterium Anabaena sp. PCC… · 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 Q8YNV6
- Elsewhere: RCSB PDB 2J5S · PDBe 2J5S · UniProt Q8YNV6
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