Research workbench
Glycoprotein B from herpes simplex virus type 1, Y179S mutant, low-pH
Analyse Glycoprotein B from herpes simplex virus type 1, Y179S mutant, low-pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NWD
- Type
- protein
- Length
- 2,410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B
- UniProt
- P06437
- Ligands
- MRY, NAG, CL
- Pockets
- 20 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein B | protein | 597 | 20% helix, 36% strand | P06437 |
| A | Envelope glycoprotein B | protein | 606 | 21% helix, 33% strand | P06437 |
| C | Envelope glycoprotein B | protein | 601 | 20% helix, 32% strand | P06437 |
| D | Envelope glycoprotein B | protein | 606 | 21% helix, 33% strand | P06437 |
Ligands and binding sites
- MRY · Meso-erythritol · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains B, D, A, C
- CL · Chloride ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.60 | 0.81 | 31 | empty |
| 2 | 121 | 0.54 | 0.82 | 28 | empty |
| 3 | 128 | 0.52 | 0.81 | 26 | empty |
| 4 | 210 | 0.51 | 0.76 | 26 | empty |
| 5 | 144 | 0.50 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- B–A · 541 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 3NWD · Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH · the same entry in another collection · chain B against B, 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 3NWD · PDBe 3NWD · UniProt P06437
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