Research workbench
Crystal structure of marinobacter subterrani acetylpolyamine amidohydrolase (msapah) complexed with 5-[(3-aminopropyl) AMINO]PENTYLBORONIC acid
Analyse Crystal structure of marinobacter subterrani acetylpolyamine amidohydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PHT
- Type
- protein
- Length
- 1,376 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylpolyamine amidohydrolase
- UniProt
- A0A0J7JFD7
- Ligands
- OKP, K, MG, ZN
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylpolyamine amidohydrolase | protein | 346 | 36% helix, 16% strand | A0A0J7JFD7 |
| B, C | Acetylpolyamine amidohydrolase | protein | 343 | 38% helix, 16% strand | A0A0J7JFD7 |
| D | Acetylpolyamine amidohydrolase | protein | 344 | 37% helix, 17% strand | A0A0J7JFD7 |
Ligands and binding sites
- OKP · {5-[(3-aminopropyl)amino]pentyl}boronic acid · ligand · 4 copies · chains A, B, D, C
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, D, C
- 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.63 | 0.82 | 35 | OKP, ZN, MG |
| 2 | 492 | 0.62 | 0.76 | 41 | empty |
| 3 | 210 | 0.62 | 0.82 | 37 | MG, OKP |
| 4 | 184 | 0.47 | 0.75 | 29 | OKP |
| 5 | 114 | 0.42 | 0.76 | 27 | OKP |
Interfaces
3 interfaces between chains.
- B–D · 2376 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 277 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 170 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6PHT · 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 6PHT · PDBe 6PHT · UniProt A0A0J7JFD7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.