Research workbench
Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of adeno-associated virus
Analyse Electron microscopy analysis of a disaccharide analog complex reveals receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J4P
- Type
- protein
- Length
- 517 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- Ligands
- GU4, YYJ, NA, MG
- Pockets
- 7 · best druggability 0.64
Structure
electron microscopy · 1 distinct chain · 3% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 517 | 3% helix, 28% strand | — |
Ligands and binding sites
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · chains A
- YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · chains A
- NA · Sodium ion · metal
- MG · Magnesium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.64 | 0.75 | 64 | empty |
| 2 | 155 | 0.46 | 0.76 | 18 | empty |
| 3 | 118 | 0.41 | 0.76 | 21 | empty |
| 4 | 113 | 0.38 | 0.74 | 20 | empty |
| 5 | 125 | 0.36 | 0.73 | 20 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3J4P · Electron Microscopy Analysis of a Disaccharide Analog complex Reveals Receptor… · 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
- Elsewhere: RCSB PDB 3J4P · PDBe 3J4P
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