MolNFT v1 · #75080 · protein
Crystal structure of a putative acetylornithine deacetylase (RPA2325) from rhodopseudomonas palustris CGA009 at 1.90 a resolution
3PFO: “Crystal structure of a putative acetylornithine deacetylase (RPA2325) from rhodopseudomonas palustris CGA009…”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.65). MolNFT v1 #75080 on GenesisL1: 3D structure…
- PDB
- 3PFO
- Type
- protein
- Length
- 852 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative acetylornithine deacetylase
- EC
- 3.5.1.16
- UniProt
- Q6N7D3
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative acetylornithine deacetylase (EC 3.5.1.16) | protein | 426 | 41% helix, 23% strand | Q6N7D3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.65 | 0.86 | 30 | empty |
| 2 | 197 | 0.63 | 0.84 | 45 | empty |
| 3 | 174 | 0.50 | 0.77 | 23 | empty |
| 4 | 166 | 0.49 | 0.77 | 22 | empty |
| 5 | 114 | 0.44 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2269 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3PFO · Crystal structure of a putative acetylornithine deacetylase (RPA2325) from… · 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 Q6N7D3
- Elsewhere: RCSB PDB 3PFO · PDBe 3PFO · UniProt Q6N7D3
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