Research workbench
Endosialidase of bacteriophage K1F in complex with oligomeric alpha-2, 8-sialic acid
Analyse Endosialidase of bacteriophage K1F in complex with oligomeric alpha-2, 8-sialic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V0F
- Type
- protein
- Length
- 3,996 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-alpha-sialidase
- EC
- 3.2.1.129
- UniProt
- Q858B1
- Ligands
- SIA, SLB, PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Endo-alpha-sialidase (EC 3.2.1.129) | protein | 666 | 3% helix, 44% strand | Q858B1 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains C, B, D, E, F
- SLB · N-acetyl-beta-neuraminic acid · sugar · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.89 | 0.93 | 156 | empty |
| 2 | 625 | 0.87 | 0.92 | 113 | empty |
| 3 | 907 | 0.84 | 0.86 | 103 | empty |
| 4 | 78 | 0.79 | 0.99 | 18 | empty |
| 5 | 74 | 0.78 | 0.99 | 18 | empty |
Interfaces
11 interfaces between chains.
- E–F · 7504 Ų buried · 156 hydrogen bonds · protein-protein
- D–E · 7473 Ų buried · 144 hydrogen bonds · protein-protein
- A–C · 7439 Ų buried · 150 hydrogen bonds · protein-protein
- D–F · 7423 Ų buried · 152 hydrogen bonds · protein-protein
- A–B · 7405 Ų buried · 144 hydrogen bonds · protein-protein
Compared structures
- 1V0F · Endosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid · 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 Q858B1
- Elsewhere: RCSB PDB 1V0F · PDBe 1V0F · UniProt Q858B1
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