Research workbench
O-glycan attached to herpes simplex virus type 1 glycoprotein gb is recognized by the ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha
Analyse O-glycan attached to herpes simplex virus type 1 glycoprotein gb is recognized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WV0
- Type
- protein
- Length
- 251 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paired immunoglobulin-like type 2 receptor alpha; Envelope glycoprotein B
- UniProt
- C9JGG1, P06437
- Ligands
- A2G, SIA, SO4
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Paired immunoglobulin-like type 2 receptor alpha | protein | 119 | 3% helix, 46% strand | C9JGG1 |
| X | Envelope glycoprotein B | protein | 7 | 0% helix, 0% strand | P06437 |
| Y | Envelope glycoprotein B | protein | 6 | 0% helix, 0% strand | P06437 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, X, B, Y
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, X, B, Y
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.34 | 0.76 | 19 | SIA |
| 2 | 66 | 0.32 | 0.75 | 19 | SIA |
Interfaces
3 interfaces between chains.
- A–X · 236 Ų buried · 1 hydrogen bond · protein-protein
- B–Y · 214 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 108 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (O-glycosylation).
Compared structures
- 3WV0 · O-glycan attached to herpes simplex virus type 1 glycoprotein gB is recognized by the Ig… · 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 C9JGG1
- Every structure of UniProt P06437
- Elsewhere: RCSB PDB 3WV0 · PDBe 3WV0 · UniProt C9JGG1 · UniProt P06437
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