Research workbench
X-ray crystal structure of acetylcholine binding protein (achbp) in complex with 4-(2-amino-6-{BIS[(PYRIDIN-2-YL)METHYL]AMINO}PYRIMIDIN- 4-YL)PHENOL
Analyse X-ray crystal structure of acetylcholine binding protein (achbp) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J5I
- Type
- protein
- Length
- 2,126 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- 6GM, NAG, PO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acetylcholine-binding protein | protein | 213 | 11% helix, 48% strand | P58154 |
| E, F, H, I, J | Acetylcholine-binding protein | protein | 212 | 11% helix, 48% strand | P58154 |
| G | Acetylcholine-binding protein | protein | 214 | 11% helix, 45% strand | P58154 |
Ligands and binding sites
- 6GM · 4-(2-amino-6-{bis[(pyridin-2-yl)methyl]amino}pyrimidin-4-yl)phenol · ligand · 10 copies · chains A, B, E, C, D, F, G, J, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, G, B, F, C, J, D, I, E, H
- PO4 · Phosphate ion · ion · 21 copies · chains A, E, B, C, D, F, G, J, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.72 | 0.87 | 30 | 6GM |
| 2 | 246 | 0.72 | 0.86 | 27 | 6GM |
| 3 | 310 | 0.71 | 0.85 | 36 | 6GM |
| 4 | 757 | 0.71 | 0.77 | 75 | empty |
| 5 | 278 | 0.71 | 0.85 | 30 | 6GM |
Interfaces
20 interfaces between chains.
- D–E · 1766 Ų buried · 30 hydrogen bonds · protein-protein
- F–J · 1714 Ų buried · 30 hydrogen bonds · protein-protein
- H–I · 1698 Ų buried · 25 hydrogen bonds · protein-protein
- F–G · 1692 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1691 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5J5I · X-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) in Complex with… · the same entry in another collection · chain J against J, TM-score 1.00
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain I against A, TM-score 0.93
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 P58154
- Elsewhere: RCSB PDB 5J5I · PDBe 5J5I · UniProt P58154
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