Research workbench
X-ray structure of acetylcholine binding protein (achbp) in complex with 6-(2-methoxyphenyl)-N4,N4-BIS[(PYRIDIN-2-YL)METHYL]PYRIMIDINE-2, 4-diamine
Analyse X-ray structure of acetylcholine binding protein (achbp) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J5H
- Type
- protein
- Length
- 2,072 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- 6GK, NAG, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 9 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein | protein | 204 | 10% helix, 50% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 211 | 9% helix, 47% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 203 | 10% helix, 49% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 207 | 11% helix, 48% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 206 | 10% helix, 42% strand | P58154 |
| F, G | Acetylcholine-binding protein | protein | 212 | 11% helix, 47% strand | P58154 |
| H | Acetylcholine-binding protein | protein | 210 | 11% helix, 48% strand | P58154 |
| I | Acetylcholine-binding protein | protein | 202 | 10% helix, 47% strand | P58154 |
| J | Acetylcholine-binding protein | protein | 205 | 11% helix, 49% strand | P58154 |
Ligands and binding sites
- 6GK · 6-(2-methoxyphenyl)-N~4~,N~4~-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, F, C, D, E, G, H, I, J
- PO4 · Phosphate ion · ion · 11 copies · chains A, E, B, C, D, F, J, G, 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 | 1158 | 0.78 | 0.80 | 108 | empty |
| 2 | 347 | 0.73 | 0.85 | 36 | 6GK |
| 3 | 772 | 0.71 | 0.78 | 83 | empty |
| 4 | 330 | 0.71 | 0.84 | 38 | 6GK |
| 5 | 249 | 0.71 | 0.86 | 28 | 6GK |
Interfaces
20 interfaces between chains.
- F–G · 1721 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1665 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1650 Ų buried · 26 hydrogen bonds · protein-protein
- F–J · 1647 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1646 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5J5H · X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPLEX WITH… · the same entry in another collection · chain I against I, TM-score 1.00
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 5J5H · PDBe 5J5H · UniProt P58154
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