MolNFT v1 · #76070 · protein
Crystal structure of H159A apah complexed with N8-acetylspermidine
3Q9C · Acetylpolyamine amidohydrolase: “Crystal structure of H159A apah complexed with N8-acetylspermidine”. X-ray diffraction, 4 ligands (Q9C, K, ZN), 20 pockets (best druggability 0.80). MolNFT v1 #76070 on GenesisL1: 3D structure…
- PDB
- 3Q9C
- 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
- Q9C, K, ZN, NA
- 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
- Q9C · N-{4-[(3-aminopropyl)amino]butyl}acetamide · ligand · 12 copies · chains A, I, B, F, C, K, D, E, H, G, L, J
- K · Potassium 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
- NA · Sodium 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 | 985 | 0.80 | 0.82 | 84 | empty |
| 2 | 1068 | 0.80 | 0.81 | 102 | empty |
| 3 | 1000 | 0.80 | 0.81 | 91 | empty |
| 4 | 1005 | 0.79 | 0.81 | 86 | empty |
| 5 | 1042 | 0.79 | 0.81 | 91 | empty |
Interfaces
27 interfaces between chains.
- C–K · 2365 Ų buried · 41 hydrogen bonds · protein-protein
- E–H · 2361 Ų buried · 41 hydrogen bonds · protein-protein
- G–L · 2339 Ų buried · 42 hydrogen bonds · protein-protein
- A–I · 2338 Ų buried · 39 hydrogen bonds · protein-protein
- D–J · 2336 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 3Q9C · Crystal Structure of H159A APAH complexed with N8-acetylspermidine · the same entry in another collection · chain K against K, 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 3Q9C · PDBe 3Q9C · UniProt Q48935
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