Research workbench
Streptococcus pneumoniae choline importer licb in lipid nanodiscs
Analyse Streptococcus pneumoniae choline importer licb in lipid nanodiscs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PAF
- Type
- protein
- Length
- 780 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody; Licb protein
- UniProt
- A0A0H2UQH5
- Ligands
- PGT
- Pockets
- 9 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Nanobody | protein | 112 | 3% helix, 52% strand | — |
| A, D | Licb protein | protein | 278 | 79% helix, 0% strand | A0A0H2UQH5 |
Ligands and binding sites
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.78 | 0.83 | 53 | empty |
| 2 | 647 | 0.78 | 0.83 | 53 | empty |
| 3 | 626 | 0.72 | 0.79 | 46 | empty |
| 4 | 604 | 0.72 | 0.79 | 42 | empty |
| 5 | 215 | 0.69 | 0.85 | 16 | PGT |
Interfaces
3 interfaces between chains.
- A–D · 865 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 396 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 394 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7PAF · Streptococcus pneumoniae choline importer LicB in lipid nanodiscs · the same entry in another collection · chain B against B, 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 A0A0H2UQH5
- Elsewhere: RCSB PDB 7PAF · PDBe 7PAF · UniProt A0A0H2UQH5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.