Research workbench
Glycoprotein B from Herpes Simplex Virus type 1, A549T Rate-of-Entry mutant, low-pH
Analyse Glycoprotein B from Herpes Simplex Virus type 1, A549T Rate-of-Entry mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L1R
- Type
- protein
- Length
- 1,216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.0255
- Source
- Human herpesvirus 1
- Molecule
- Envelope glycoprotein B
- UniProt
- P06437
- Ligands
- NAG, CL
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · resolution 3.0255 · 1 distinct chain · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Envelope glycoprotein B | protein | 608 | 23% helix, 35% strand | P06437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.56 | 0.81 | 27 | empty |
| 2 | 107 | 0.52 | 0.82 | 21 | empty |
| 3 | 94 | 0.41 | 0.78 | 20 | empty |
| 4 | 98 | 0.38 | 0.75 | 12 | empty |
| 5 | 90 | 0.38 | 0.76 | 12 | empty |
Modifications
Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4L1R · Glycoprotein B from herpes simplex virus type 1, A549T rate-of-entry mutant, low-pH · 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 P06437
- Elsewhere: RCSB PDB 4L1R · PDBe 4L1R · UniProt P06437
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