MolNFT v1 · #160369 · protein
Crystal structure of marinobacter subterrani acetylpolyamine amidohydrolase (msapah) complexed with 8-amino-N-hydroxyoctanamide
6PID: “Crystal structure of marinobacter subterrani acetylpolyamine amidohydrolase (msapah) complexed with…”. X-ray diffraction, 4 ligands (OKS, K, MG), 2 pockets (best druggability 0.62). MolNFT v1 #160369 on GenesisL1: 3D structure…
- PDB
- 6PID
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylpolyamine amidohydrolase
- UniProt
- A0A0J7JFD7
- Ligands
- OKS, K, MG, ZN
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetylpolyamine amidohydrolase | protein | 346 | 38% helix, 17% strand | A0A0J7JFD7 |
Ligands and binding sites
- OKS · 8-amino-N-hydroxyoctanamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 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 | 230 | 0.62 | 0.81 | 35 | MG, OKS |
| 2 | 217 | 0.59 | 0.80 | 31 | OKS, MG |
Interfaces
1 interface between chains.
- A–B · 2422 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 6PID · 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 6PID · PDBe 6PID · UniProt A0A0J7JFD7
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