MolNFT v1 · #112745 · protein
Crystal structure of acetylpolyamine amidohydrolase from mycoplana ramosa in complex with a hydroxamate inhibitor
4ZUP · Acetylpolyamine aminohydrolase: “Crystal structure of acetylpolyamine amidohydrolase from mycoplana ramosa in complex with a hydroxamate…”. X-ray diffraction, 4 ligands (5XA, ZN, K), 2 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 4ZUP
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylpolyamine aminohydrolase
- UniProt
- Q48935
- Ligands
- 5XA, ZN, K, NO3
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetylpolyamine aminohydrolase | protein | 341 | 38% helix, 16% strand | Q48935 |
Ligands and binding sites
- 5XA · 5-amino-N-hydroxypentanamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- NO3 · Nitrate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.75 | 0.89 | 39 | 5XA |
| 2 | 228 | 0.73 | 0.88 | 37 | ZN, 5XA |
Interfaces
1 interface between chains.
- A–B · 2295 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4ZUP · Crystal structure of acetylpolyamine amidohydrolase from Mycoplana ramosa in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q48935 · AlphaFold monomer V2.0 prediction for acetylpolyamine amidohydrolase (Q48935) · a predicted model of the same protein · chain B 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 Q48935
- Elsewhere: RCSB PDB 4ZUP · PDBe 4ZUP · UniProt Q48935
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