Research workbench
Agao in covalent complex with the inhibitor noba ("4-(2-naphthyloxy)- 2-butyn-1-amine")
Analyse Agao in covalent complex with the inhibitor noba ("4-(2-naphthyloxy)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SII
- Type
- protein
- Length
- 620 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylethylamine oxidase
- EC
- 1.4.3.6
- UniProt
- P46881
- Ligands
- CU, NA, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylethylamine oxidase (EC 1.4.3.6) | protein | 620 | 13% helix, 43% strand | P46881 |
Ligands and binding sites
- CU · Copper (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.67 | 0.83 | 58 | empty |
| 2 | 65 | 0.51 | 0.85 | 17 | empty |
| 3 | 70 | 0.43 | 0.81 | 17 | empty |
| 4 | 93 | 0.37 | 0.75 | 22 | empty |
| 5 | 81 | 0.35 | 0.75 | 21 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 1SII · AGAO in covalent complex with the inhibitor NOBA ("4-(2-naphthyloxy)-2-butyn-1-amine") · 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 P46881
- Elsewhere: RCSB PDB 1SII · PDBe 1SII · UniProt P46881
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