Research workbench
Crystal structure of the colanidase tailspike protein GP150 of phage PHI92 complexed with one repeating unit of colanic acid
Analyse Crystal structure of the colanidase tailspike protein GP150 of phage PHI92… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E0W
- Type
- protein
- Length
- 1,204 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophage PHI92 GP150
- UniProt
- I7I026
- Ligands
- HLA, FUC, BGC, GLA, BDP, MG, SO4
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bacteriophage PHI92 GP150 | protein | 602 | 6% helix, 47% strand | I7I026 |
Ligands and binding sites
- HLA · 1,5-anhydro-4,6-O-[(1R)-1-carboxyethylidene]-D-galactitol · ligand · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
- PG4 · Tetraethylene glycol · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.57 | 0.76 | 39 | empty |
| 2 | 372 | 0.57 | 0.75 | 45 | empty |
| 3 | 153 | 0.42 | 0.74 | 25 | BGC, FUC, SO4 |
| 4 | 146 | 0.38 | 0.73 | 26 | BGC, FUC, SO4 |
| 5 | 96 | 0.33 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6E0W · Crystal structure of the colanidase tailspike protein gp150 of Phage Phi92 complexed with… · 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 I7I026
- Elsewhere: RCSB PDB 6E0W · PDBe 6E0W · UniProt I7I026
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