MolNFT v1 · #160368 · protein
Crystal structure of marinobacter subterrani acetylpolyamine amidohydrolase (msapah) complexed with 6-amino-N-hydroxyhexanamide
6PIC: “Crystal structure of marinobacter subterrani acetylpolyamine amidohydrolase (msapah) complexed with…”. X-ray diffraction, 4 ligands (6XA, K, ZN), 20 pockets (best druggability 0.63). MolNFT v1 #160368 on GenesisL1: 3D structure…
- PDB
- 6PIC
- Type
- protein
- Length
- 2,757 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylpolyamine amidohydrolase
- UniProt
- A0A0J7JFD7
- Ligands
- 6XA, K, ZN, MG
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylpolyamine amidohydrolase | protein | 343 | 38% helix, 16% strand | A0A0J7JFD7 |
| B, C, D, F, G, H | Acetylpolyamine amidohydrolase | protein | 345 | 38% helix, 16% strand | A0A0J7JFD7 |
| E | Acetylpolyamine amidohydrolase | protein | 344 | 38% helix, 16% strand | A0A0J7JFD7 |
Ligands and binding sites
- 6XA · 6-amino-N-hydroxyhexanamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- K · Potassium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.63 | 0.75 | 45 | empty |
| 2 | 232 | 0.63 | 0.82 | 27 | empty |
| 3 | 250 | 0.57 | 0.78 | 25 | empty |
| 4 | 229 | 0.52 | 0.76 | 37 | 6XA |
| 5 | 236 | 0.51 | 0.75 | 38 | 6XA |
Interfaces
8 interfaces between chains.
- A–G · 340 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 316 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 276 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 275 Ų buried · 2 hydrogen bonds · protein-protein
- A–H · 246 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6PIC · 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 6PIC · PDBe 6PIC · UniProt A0A0J7JFD7
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