Research workbench
Crystal structure of dettilon tailspike protein (GP208)
Analyse Crystal structure of dettilon tailspike protein (GP208) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F7K
- Type
- protein
- Length
- 3,281 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tailspike
- UniProt
- A0A0C5PVE3
- Ligands
- RAM, BMA, GLA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tailspike | protein | 546 | 8% helix, 45% strand | A0A0C5PVE3 |
| B, C, D, F, G | Tailspike | protein | 547 | 8% helix, 46% strand | A0A0C5PVE3 |
Ligands and binding sites
- RAM · alpha-L-rhamnopyranose · sugar · 12 copies · chains A, B, C, D, F, G
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, B, C, D, F, G
- GLA · alpha-D-galactopyranose · sugar · 12 copies · chains A, B, C, D, F, G
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.89 | 0.91 | 128 | empty |
| 2 | 1185 | 0.89 | 0.90 | 133 | empty |
| 3 | 176 | 0.83 | 0.97 | 28 | empty |
| 4 | 152 | 0.82 | 0.98 | 28 | empty |
| 5 | 179 | 0.82 | 0.96 | 18 | empty |
Interfaces
7 interfaces between chains.
- B–C · 3103 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 3094 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3091 Ų buried · 43 hydrogen bonds · protein-protein
- A–F · 3089 Ų buried · 41 hydrogen bonds · protein-protein
- A–G · 3051 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 6F7K · Crystal structure of Dettilon tailspike protein (gp208) · 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 A0A0C5PVE3
- Elsewhere: RCSB PDB 6F7K · PDBe 6F7K · UniProt A0A0C5PVE3
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