Research workbench
Ghgl of varicella-zoster virus in complex with human neutralizing antibodies
Analyse Ghgl of varicella-zoster virus in complex with human neutralizing antibodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XI5
- Type
- protein
- Length
- 1,274 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Fab-94 light chain; Fab-94 heavy chain
- UniProt
- Q775J3, Q9J3N1
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 728 | 34% helix, 20% strand | Q775J3 |
| B | Envelope glycoprotein L | protein | 132 | 27% helix, 14% strand | Q9J3N1 |
| C | Fab-94 light chain | protein | 206 | 3% helix, 41% strand | — |
| D | Fab-94 heavy chain | protein | 208 | 0% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.71 | 0.83 | 41 | empty |
| 2 | 424 | 0.68 | 0.80 | 42 | empty |
| 3 | 269 | 0.60 | 0.79 | 36 | empty |
| 4 | 227 | 0.57 | 0.79 | 35 | empty |
| 5 | 288 | 0.57 | 0.77 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3545 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2076 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 513 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 253 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4XI5 · gHgL of varicella-zoster virus in complex with human neutralizing antibodies · 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 Q775J3
- Every structure of UniProt Q9J3N1
- Elsewhere: RCSB PDB 4XI5 · PDBe 4XI5 · UniProt Q775J3 · UniProt Q9J3N1
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