Research workbench
Engineered ls-achbp with ALPHA4-ALPHA4 binding pocket in complex with NS3920
Analyse Engineered ls-achbp with ALPHA4-ALPHA4 binding pocket in complex with NS3920 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UM3
- Type
- protein
- Length
- 7,922 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine binding protein
- UniProt
- P58154
- Ligands
- 09R, NAG, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 27 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine binding protein | protein | 201 | 8% helix, 46% strand | P58154 |
| B, k | Acetylcholine binding protein | protein | 198 | 9% helix, 48% strand | P58154 |
| C | Acetylcholine binding protein | protein | 201 | 8% helix, 49% strand | P58154 |
| D, m | Acetylcholine binding protein | protein | 201 | 8% helix, 49% strand | P58154 |
| E | Acetylcholine binding protein | protein | 195 | 9% helix, 50% strand | P58154 |
| F, Z | Acetylcholine binding protein | protein | 196 | 9% helix, 47% strand | P58154 |
| G, I, J, l | Acetylcholine binding protein | protein | 200 | 9% helix, 48% strand | P58154 |
| H, K, Y, i | Acetylcholine binding protein | protein | 197 | 9% helix, 47% strand | P58154 |
| L | Acetylcholine binding protein | protein | 195 | 9% helix, 48% strand | P58154 |
| M | Acetylcholine binding protein | protein | 198 | 9% helix, 47% strand | P58154 |
| N, Q, n | Acetylcholine binding protein | protein | 196 | 9% helix, 47% strand | P58154 |
| O | Acetylcholine binding protein | protein | 196 | 9% helix, 49% strand | P58154 |
| P | Acetylcholine binding protein | protein | 201 | 8% helix, 46% strand | P58154 |
| R | Acetylcholine binding protein | protein | 198 | 9% helix, 48% strand | P58154 |
| S | Acetylcholine binding protein | protein | 201 | 8% helix, 47% strand | P58154 |
| T | Acetylcholine binding protein | protein | 194 | 9% helix, 50% strand | P58154 |
| U | Acetylcholine binding protein | protein | 197 | 9% helix, 49% strand | P58154 |
| V | Acetylcholine binding protein | protein | 199 | 9% helix, 49% strand | P58154 |
| W | Acetylcholine binding protein | protein | 197 | 9% helix, 47% strand | P58154 |
| X | Acetylcholine binding protein | protein | 202 | 8% helix, 47% strand | P58154 |
| a | Acetylcholine binding protein | protein | 197 | 9% helix, 47% strand | P58154 |
| b, e | Acetylcholine binding protein | protein | 198 | 9% helix, 49% strand | P58154 |
| c | Acetylcholine binding protein | protein | 200 | 9% helix, 47% strand | P58154 |
| d | Acetylcholine binding protein | protein | 198 | 9% helix, 47% strand | P58154 |
| f | Acetylcholine binding protein | protein | 195 | 9% helix, 48% strand | P58154 |
| g, j | Acetylcholine binding protein | protein | 198 | 9% helix, 48% strand | P58154 |
| h | Acetylcholine binding protein | protein | 199 | 9% helix, 47% strand | P58154 |
Ligands and binding sites
- 09R · 1-(6-bromopyridin-3-yl)-1,4-diazepane · ligand · 40 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, F, O, d
- SO4 · Sulfate ion · ion · chains U, V
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 | 546 | 0.78 | 0.85 | 62 | empty |
| 2 | 1026 | 0.78 | 0.80 | 82 | empty |
| 3 | 761 | 0.78 | 0.82 | 73 | empty |
| 4 | 780 | 0.78 | 0.82 | 59 | empty |
| 5 | 93 | 0.77 | 0.98 | 19 | 09R |
Interfaces
78 interfaces between chains.
- D–E · 1483 Ų buried · 17 hydrogen bonds · protein-protein
- S–T · 1471 Ų buried · 18 hydrogen bonds · protein-protein
- V–W · 1467 Ų buried · 19 hydrogen bonds · protein-protein
- F–J · 1457 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1450 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 79 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4UM3 · Engineered Ls-AChBP with alpha4-alpha4 binding pocket in complex with NS3920 · 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 4UM3 · PDBe 4UM3 · UniProt P58154
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