MolNFT v1 · #122965 · protein
X-ray crystal structure of acetylcholine binding protein (achbp) in complex with N4,N4-BIS[(PYRIDIN-2-YL)METHYL]-6-(thiophen-3-yl) pyrimidine-2,4-diamine
5J5F · Acetylcholine-binding protein: “X-ray crystal structure of acetylcholine binding protein (achbp) in complex with…”. X-ray diffraction, 3 ligands (6GH, NAG, PO4), 20 pockets (best druggability 0.73). MolNFT v1 #122965 on GenesisL1…
- PDB
- 5J5F
- Type
- protein
- Length
- 2,136 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- 6GH, NAG, PO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein | protein | 212 | 12% helix, 47% strand | P58154 |
| B, C, H, I, J | Acetylcholine-binding protein | protein | 213 | 11% helix, 48% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 216 | 11% helix, 47% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 218 | 11% helix, 48% strand | P58154 |
| F | Acetylcholine-binding protein | protein | 213 | 11% helix, 47% strand | P58154 |
| G | Acetylcholine-binding protein | protein | 212 | 12% helix, 48% strand | P58154 |
Ligands and binding sites
- 6GH · N~4~,N~4~-bis[(pyridin-2-yl)methyl]-6-(thiophen-3-yl)pyrimidine-2,4-diamine · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, G, B, F, C, D, I, E, H, J
- PO4 · Phosphate ion · ion · 11 copies · chains A, E, B, C, D, F, J, G, H, I
- GOL · Glycerol · additive · 2 copies · chains F, H, I
- DMS · Dimethyl sulfoxide · additive · chains E, H
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 | 277 | 0.73 | 0.86 | 32 | 6GH |
| 2 | 276 | 0.72 | 0.86 | 33 | 6GH |
| 3 | 254 | 0.72 | 0.86 | 31 | 6GH |
| 4 | 319 | 0.72 | 0.85 | 42 | 6GH |
| 5 | 230 | 0.71 | 0.87 | 27 | 6GH |
Interfaces
20 interfaces between chains.
- G–H · 1787 Ų buried · 30 hydrogen bonds · protein-protein
- I–J · 1735 Ų buried · 34 hydrogen bonds · protein-protein
- H–I · 1697 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1687 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 1678 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5J5F · 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 A 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 5J5F · PDBe 5J5F · UniProt P58154
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