MolNFT v1 · #51847 · protein
Tailspike protein of E.COLI bacteriophage HK620 in complex with hexasaccharide
2VJJ: “Tailspike protein of E.COLI bacteriophage HK620 in complex with hexasaccharide”. X-ray diffraction, 7 ligands (NAG, GLC, GAL), 3 pockets (best druggability 0.50). MolNFT v1 #51847 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VJJ
- Type
- protein
- Length
- 598 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tailspike protein
- UniProt
- Q9AYY6
- Ligands
- NAG, GLC, GAL, RAM, CA, K, CL
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tailspike protein | protein | 598 | 9% helix, 43% strand | Q9AYY6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- RAM · alpha-L-rhamnopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.50 | 0.77 | 42 | NAG, GLC |
| 2 | 123 | 0.43 | 0.76 | 21 | RAM, NAG, K |
| 3 | 124 | 0.39 | 0.75 | 17 | empty |
Compared structures
- 2VJJ · Tailspike protein of E.COLI bacteriophage HK620 in complex with hexasaccharide · 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 Q9AYY6
- Elsewhere: RCSB PDB 2VJJ · PDBe 2VJJ · UniProt Q9AYY6
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