Research workbench
Capitella teleta achbp in complex with lobeline
Analyse Capitella teleta achbp in complex with lobeline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AFH
- Type
- protein
- Length
- 1,064 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Achbp
- Ligands
- L0B, NAG, BMA, MAN
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Achbp | protein | 213 | 13% helix, 47% strand | — |
| E | Achbp | protein | 212 | 13% helix, 47% strand | — |
Ligands and binding sites
- L0B · Alpha-Lobeline · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, E, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, E
- MAN · alpha-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.75 | 0.86 | 49 | L0B |
| 2 | 370 | 0.75 | 0.86 | 51 | L0B |
| 3 | 418 | 0.74 | 0.84 | 54 | L0B |
| 4 | 211 | 0.74 | 0.89 | 32 | L0B |
| 5 | 248 | 0.73 | 0.87 | 39 | L0B |
Interfaces
5 interfaces between chains.
- B–C · 1632 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1593 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1591 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1571 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1567 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4AFH · Capitella teleta AChBP in complex with lobeline · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 4AFH · PDBe 4AFH
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