MolNFT v1 · #76072 · protein
Crystal structure of H159A apah complexed with acetylspermine
3Q9E · Acetylpolyamine amidohydrolase: “Crystal structure of H159A apah complexed with acetylspermine”. X-ray diffraction, 4 ligands (SP5, K, NA), 20 pockets (best druggability 0.80). MolNFT v1 #76072 on GenesisL1: 3D structure, binding…
- PDB
- 3Q9E
- Type
- protein
- Length
- 4,092 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylpolyamine amidohydrolase
- UniProt
- Q48935
- Ligands
- SP5, K, NA, ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Acetylpolyamine amidohydrolase | protein | 341 | 38% helix, 18% strand | Q48935 |
Ligands and binding sites
- SP5 · N-[3-({4-[(3-aminopropyl)amino]butyl}amino) propyl]acetamide · ligand · 12 copies · chains A, I, B, F, C, K, D, J, E, H, G, L
- K · Potassium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.80 | 0.82 | 84 | empty |
| 2 | 1025 | 0.80 | 0.81 | 95 | empty |
| 3 | 979 | 0.80 | 0.82 | 95 | empty |
| 4 | 1033 | 0.79 | 0.81 | 96 | empty |
| 5 | 1057 | 0.79 | 0.81 | 97 | empty |
Interfaces
27 interfaces between chains.
- E–H · 2329 Ų buried · 48 hydrogen bonds · protein-protein
- G–L · 2328 Ų buried · 43 hydrogen bonds · protein-protein
- A–I · 2326 Ų buried · 40 hydrogen bonds · protein-protein
- D–J · 2324 Ų buried · 39 hydrogen bonds · protein-protein
- C–K · 2320 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 3Q9E · Crystal structure of H159A APAH complexed with acetylspermine · the same entry in another collection · chain L against L, 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 3Q9E · PDBe 3Q9E · UniProt Q48935
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