Research workbench
Lymnaea stagnalis acetylcholine binding protein in complex with 3- [(4E)-4-[(3-methylimidazol-4-YL)METHYLENE]-2,3-dihydropyrrol-5- YL]PYRIDINE
Analyse Lymnaea stagnalis acetylcholine binding protein in complex with 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZR6
- Type
- protein
- Length
- 983 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- 4QW
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein | protein | 195 | 8% helix, 49% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 192 | 8% helix, 48% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 198 | 9% helix, 49% strand | P58154 |
| D, E | Acetylcholine-binding protein | protein | 199 | 9% helix, 49% strand | P58154 |
Ligands and binding sites
- 4QW · 3-{(4E)-4-[(1-methyl-1H-imidazol-5-yl)methylidene]-3,4-dihydro-2H-pyrrol-5-yl}pyridine · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.72 | 0.82 | 63 | 4QW |
| 2 | 533 | 0.69 | 0.79 | 54 | empty |
| 3 | 514 | 0.69 | 0.79 | 62 | empty |
| 4 | 445 | 0.68 | 0.79 | 49 | empty |
| 5 | 304 | 0.68 | 0.83 | 43 | 4QW |
Interfaces
5 interfaces between chains.
- C–D · 1233 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1165 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1117 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1062 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1048 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4ZR6 · Lymnaea Stagnalis Acetylcholine Binding Protein in Complex with… · the same entry in another collection · chain E against E, TM-score 1.00
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 4ZR6 · PDBe 4ZR6 · UniProt P58154
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