Research workbench
Crystal structure of ganp, a glucose-galactose binding protein from geobacillus stearothermophilus, in complex with galactose
Analyse Crystal structure of ganp, a glucose-galactose binding protein from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GT9
- Type
- protein
- Length
- 1,132 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sugar binding protein
- UniProt
- W8QN64
- Ligands
- GAL, SO4
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative sugar binding protein | protein | 283 | 45% helix, 20% strand | W8QN64 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.70 | 0.81 | 58 | empty |
| 2 | 425 | 0.68 | 0.80 | 39 | empty |
| 3 | 362 | 0.66 | 0.80 | 46 | empty |
| 4 | 371 | 0.66 | 0.80 | 38 | empty |
| 5 | 248 | 0.62 | 0.81 | 38 | empty |
Interfaces
5 interfaces between chains.
- B–C · 962 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 955 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 403 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 214 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 73 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6GT9 · Crystal structure of GanP, a glucose-galactose binding protein from Geobacillus… · 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 W8QN64
- Elsewhere: RCSB PDB 6GT9 · PDBe 6GT9 · UniProt W8QN64
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