MolNFT v1 · #150510 · protein
Tailspike protein mutant E372Q (delta N471/S472) of E. COLI bacteriophage HK620 in complex with pentasaccharide
6GVR · Tail spike protein: “Tailspike protein mutant E372Q (delta N471/S472) of E. COLI bacteriophage HK620 in complex with…”. X-ray diffraction, 6 ligands (NDG, GLA, GLC), 3 pockets (best druggability 0.42). MolNFT v1 #150510 on…
- PDB
- 6GVR
- Type
- protein
- Length
- 597 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tail spike protein
- UniProt
- Q9AYY6
- Ligands
- NDG, GLA, GLC, RAM, NAG, NA
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tail spike protein | protein | 597 | 10% helix, 44% strand | Q9AYY6 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- GLA · alpha-D-galactopyranose · sugar · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- RAM · alpha-L-rhamnopyranose · sugar · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- FMT · Formic acid · additive · 4 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.42 | 0.77 | 18 | RAM, NAG |
| 2 | 115 | 0.37 | 0.74 | 34 | NDG |
| 3 | 94 | 0.34 | 0.74 | 18 | empty |
Compared structures
- 6GVR · Tailspike protein mutant E372Q (delta N471/S472) of E. COLI bacteriophage HK620 in… · 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 6GVR · PDBe 6GVR · UniProt Q9AYY6
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