MolNFT v1 · #160357 · protein
Crystal structure of marinobacter subterrani acetylpolyamine amidohydrolase (msapah) complexed with 4-(dimethylamino)-N-[7- hydroxyamino)-7-OXOHEPTYL]BENZAMIDE
6PI1: “Crystal structure of marinobacter subterrani acetylpolyamine amidohydrolase (msapah) complexed with…”. X-ray diffraction, 4 ligands (B3N, K, MG), 10 pockets (best druggability 0.72). MolNFT v1 #160357 on GenesisL1: 3D structure…
- PDB
- 6PI1
- Type
- protein
- Length
- 1,381 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylpolyamine amidohydrolase
- UniProt
- A0A0J7JFD7
- Ligands
- B3N, K, MG, ZN
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylpolyamine amidohydrolase | protein | 345 | 38% helix, 17% strand | A0A0J7JFD7 |
| B, D | Acetylpolyamine amidohydrolase | protein | 346 | 35% helix, 16% strand | A0A0J7JFD7 |
| C | Acetylpolyamine amidohydrolase | protein | 344 | 38% helix, 16% strand | A0A0J7JFD7 |
Ligands and binding sites
- B3N · 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.72 | 0.83 | 52 | empty |
| 2 | 225 | 0.63 | 0.82 | 37 | MG, B3N |
| 3 | 203 | 0.62 | 0.82 | 34 | ZN, B3N, MG |
| 4 | 224 | 0.52 | 0.76 | 40 | B3N |
| 5 | 172 | 0.50 | 0.77 | 33 | ZN, B3N |
Interfaces
3 interfaces between chains.
- A–B · 2381 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 309 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 154 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PI1 · Crystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH)… · 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 A0A0J7JFD7
- Elsewhere: RCSB PDB 6PI1 · PDBe 6PI1 · UniProt A0A0J7JFD7
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