Research workbench
Agao in complex with WC6B (ru-wire inhibitor, 6-carbon linker, data set B)
Analyse Agao in complex with WC6B (ru-wire inhibitor, 6-carbon linker, data set B) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CFL
- 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
- R6A, CU, NA, SO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylethylamine oxidase (EC 1.4.3.6) | protein | 620 | 13% helix, 42% strand | P46881 |
Ligands and binding sites
- R6A · Ruthenium wire, 6 carbon linker · ligand · chains A
- CU · Copper (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.70 | 0.84 | 62 | empty |
| 2 | 196 | 0.52 | 0.77 | 30 | empty |
| 3 | 61 | 0.51 | 0.86 | 17 | empty |
| 4 | 66 | 0.42 | 0.82 | 17 | empty |
| 5 | 80 | 0.35 | 0.75 | 23 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 2CFL · AGAO in complex with wc6b (Ru-wire inhibitor, 6-carbon linker, data set b) · 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 2CFL · PDBe 2CFL · UniProt P46881
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