MolNFT v2 · #218997 · protein
Beta-keto acid cleavage enzyme from Paracoccus denitrificans with bound malonate and Coenzyme A
8RIP · 3-keto-5-aminohexanoate cleavage protein: “Beta-keto acid cleavage enzyme from Paracoccus denitrificans with bound malonate and Coenzyme A”. X-ray diffraction at 1.81, 2 ligands (COA, ZN), 7 pockets (best druggability 0.75). MolNFT…
- PDB
- 8RIP
- Type
- protein
- Length
- 1,237 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.81
- Source
- Paracoccus denitrificans PD1222
- Molecule
- 3-keto-5-aminohexanoate cleavage protein
- UniProt
- A1B802
- Ligands
- COA, ZN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.81 · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-keto-5-aminohexanoate cleavage protein | protein | 311 | 42% helix, 19% strand | A1B802 |
| B | 3-keto-5-aminohexanoate cleavage protein | protein | 310 | 42% helix, 18% strand | A1B802 |
| C, D | 3-keto-5-aminohexanoate cleavage protein | protein | 308 | 43% helix, 19% strand | A1B802 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, C, B
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MLI · Malonate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.75 | 0.78 | 100 | MLI |
| 2 | 781 | 0.74 | 0.79 | 87 | MLI, COA |
| 3 | 422 | 0.72 | 0.83 | 52 | MLI, COA, ZN |
| 4 | 453 | 0.72 | 0.81 | 53 | MLI, ZN |
| 5 | 391 | 0.59 | 0.76 | 45 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1492 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1481 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 888 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 836 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
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 A1B802
- Elsewhere: RCSB PDB 8RIP · PDBe 8RIP · UniProt A1B802
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