MolNFT v1 · #76073 · protein
Crystal structure of apah complexed with caps
3Q9F · Acetylpolyamine amidohydrolase: “Crystal structure of apah complexed with caps”. X-ray diffraction, 4 ligands (K, NA, ZN), 20 pockets (best druggability 0.80). MolNFT v1 #76073 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3Q9F
- Type
- protein
- Length
- 4,090 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylpolyamine amidohydrolase
- UniProt
- Q48935
- Ligands
- K, NA, ZN, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, K, L | Acetylpolyamine amidohydrolase | protein | 341 | 38% helix, 18% strand | Q48935 |
| I, J | Acetylpolyamine amidohydrolase | protein | 340 | 39% helix, 16% strand | Q48935 |
Ligands and binding sites
- K · Potassium ion · metal · 20 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
- PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 12 copies · chains A, I, B, C, D, J, E, F, G, H, 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 | 1082 | 0.80 | 0.81 | 98 | empty |
| 2 | 1036 | 0.79 | 0.81 | 93 | empty |
| 3 | 982 | 0.79 | 0.81 | 87 | empty |
| 4 | 961 | 0.79 | 0.81 | 90 | empty |
| 5 | 1038 | 0.79 | 0.80 | 91 | empty |
Interfaces
27 interfaces between chains.
- E–H · 2310 Ų buried · 39 hydrogen bonds · protein-protein
- B–F · 2305 Ų buried · 37 hydrogen bonds · protein-protein
- D–J · 2298 Ų buried · 40 hydrogen bonds · protein-protein
- C–K · 2295 Ų buried · 41 hydrogen bonds · protein-protein
- A–I · 2292 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3Q9F · Crystal Structure of APAH complexed with CAPS · 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 3Q9F · PDBe 3Q9F · UniProt Q48935
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