MolNFT v1 · #84206 · protein
Crystal structure of ls-achbp complexed with carbamoylcholine analogue 3-(DIMETHYLAMINO)BUTYL dimethylcarbamate (dmabc)
3ZDG · Acetylcholine binding protein: “Crystal structure of ls-achbp complexed with carbamoylcholine analogue 3-(DIMETHYLAMINO)BUTYL…”. X-ray diffraction, 3 ligands (XRX, NAG, SO4), 20 pockets (best druggability 0.77). MolNFT v1 #84206 on…
- PDB
- 3ZDG
- Type
- protein
- Length
- 3,991 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine binding protein
- UniProt
- P58154
- Ligands
- XRX, NAG, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G, H, J, O, T | Acetylcholine binding protein | protein | 200 | 9% helix, 48% strand | P58154 |
| B | Acetylcholine binding protein | protein | 201 | 8% helix, 47% strand | P58154 |
| C | Acetylcholine binding protein | protein | 204 | 8% helix, 48% strand | P58154 |
| D, E, I, K, L, M, P, R | Acetylcholine binding protein | protein | 199 | 9% helix, 48% strand | P58154 |
| N | Acetylcholine binding protein | protein | 197 | 9% helix, 48% strand | P58154 |
| Q | Acetylcholine binding protein | protein | 198 | 9% helix, 48% strand | P58154 |
| S | Acetylcholine binding protein | protein | 199 | 9% helix, 48% strand | P58154 |
Ligands and binding sites
- XRX · 3-(dimethylamino)butyl dimethylcarbamate · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains M, O, F, P
- SO4 · Sulfate ion · ion · 20 copies · chains A, E, B, C, D, F, G, J, H, I, K, O, L, M, N, P, Q, R
- PEG · Di(hydroxyethyl)ether · additive · chains M
- 1PE · Pentaethylene glycol · additive · chains R
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 | 1118 | 0.77 | 0.79 | 117 | SO4, XRX |
| 2 | 1092 | 0.76 | 0.79 | 85 | XRX, SO4 |
| 3 | 494 | 0.73 | 0.82 | 49 | empty |
| 4 | 155 | 0.69 | 0.88 | 29 | XRX |
| 5 | 136 | 0.68 | 0.88 | 22 | XRX |
Interfaces
29 interfaces between chains.
- B–C · 1422 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1411 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1409 Ų buried · 21 hydrogen bonds · protein-protein
- R–S · 1406 Ų buried · 19 hydrogen bonds · protein-protein
- K–O · 1401 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3ZDG · Crystal Structure of Ls-AChBP complexed with carbamoylcholine analogue… · the same entry in another collection · chain K against K, TM-score 1.00
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 3ZDG · PDBe 3ZDG · UniProt P58154
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