MolNFT v1 · #107753 · protein
Engineered ls-achbp with ALPHA4-ALPHA4 binding pocket in complex with NS3573
4UM1 · Acetylcholine-binding protein: “Engineered ls-achbp with ALPHA4-ALPHA4 binding pocket in complex with NS3573”. X-ray diffraction, 2 ligands (09P, NAG), 19 pockets (best druggability 0.70). MolNFT v1 #107753 on GenesisL1: 3D…
- PDB
- 4UM1
- Type
- protein
- Length
- 1,004 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- 09P, NAG
- Pockets
- 19 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein | protein | 200 | 9% helix, 48% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 200 | 9% helix, 47% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 199 | 9% helix, 48% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 204 | 10% helix, 46% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 201 | 8% helix, 48% strand | P58154 |
Ligands and binding sites
- 09P · 1-(5-ethoxypyridin-3-yl)-1,4-diazepane · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.70 | 0.88 | 30 | 09P |
| 2 | 147 | 0.70 | 0.89 | 23 | 09P |
| 3 | 160 | 0.69 | 0.88 | 24 | 09P |
| 4 | 176 | 0.69 | 0.87 | 28 | 09P |
| 5 | 175 | 0.69 | 0.87 | 31 | 09P |
Interfaces
5 interfaces between chains.
- C–D · 1359 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1353 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1329 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1325 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1323 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4UM1 · Engineered Ls-AChBP with alpha4-alpha4 binding pocket in complex with NS3573 · 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 C 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 4UM1 · PDBe 4UM1 · UniProt P58154
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