Research workbench
Lactose permease complex with thiodigalactoside and nanobody 9043
Analyse Lactose permease complex with thiodigalactoside and nanobody 9043 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VBG
- Type
- protein
- Length
- 1,031 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactoside permease; Nanobody 9043
- UniProt
- C6FW78
- Ligands
- BNG, YIO, GAL
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactoside permease | protein | 396 | 82% helix, 0% strand | C6FW78 |
| C | Nanobody 9043 | protein | 121 | 5% helix, 54% strand | — |
| B | Galactoside permease | protein | 397 | 83% helix, 0% strand | C6FW78 |
| D | Nanobody 9043 | protein | 117 | 5% helix, 57% strand | — |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 9 copies · chains A, C, B, D
- YIO · 1-thio-beta-D-galactopyranose · ligand · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.88 | 0.89 | 97 | YIO, GAL, BNG |
| 2 | 1125 | 0.88 | 0.89 | 87 | YIO, GAL, BNG |
| 3 | 855 | 0.74 | 0.77 | 45 | empty |
| 4 | 137 | 0.52 | 0.80 | 20 | empty |
| 5 | 110 | 0.47 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 898 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 892 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 567 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6VBG · Lactose permease complex with thiodigalactoside and nanobody 9043 · 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
- Every structure of UniProt C6FW78
- Elsewhere: RCSB PDB 6VBG · PDBe 6VBG · UniProt C6FW78
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