MolNFT v1 · #109938 · protein
Ghgl of varicella-zoster virus in complex with human neutralizing antibodies.
4XHJ · Envelope glycoprotein H: “Ghgl of varicella-zoster virus in complex with human neutralizing antibodies.”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.73). MolNFT v1 #109938 on GenesisL1: 3D…
- PDB
- 4XHJ
- Type
- protein
- Length
- 2,512 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Fab-rc light chain; Fab-rc heavy chain
- UniProt
- Q775J3, Q9J3N1
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 729 | 37% helix, 20% strand | Q775J3 |
| B | Envelope glycoprotein L | protein | 132 | 22% helix, 16% strand | Q9J3N1 |
| C | Fab-rc light chain | protein | 207 | 3% helix, 46% strand | — |
| D | Fab-rc heavy chain | protein | 207 | 1% helix, 44% strand | — |
| E | Envelope glycoprotein H | protein | 705 | 37% helix, 20% strand | Q775J3 |
| F | Envelope glycoprotein L | protein | 130 | 22% helix, 14% strand | Q9J3N1 |
| G | Fab-rc light chain | protein | 196 | 4% helix, 45% strand | — |
| H | Fab-rc heavy chain | protein | 206 | 1% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, E, F
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.73 | 0.87 | 53 | empty |
| 2 | 481 | 0.72 | 0.81 | 42 | empty |
| 3 | 501 | 0.69 | 0.80 | 44 | empty |
| 4 | 260 | 0.66 | 0.83 | 49 | empty |
| 5 | 312 | 0.65 | 0.81 | 38 | empty |
Interfaces
14 interfaces between chains.
- A–B · 3521 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 3448 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1841 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1768 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 435 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4XHJ · 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 4XHJ · PDBe 4XHJ · UniProt Q775J3 · UniProt Q9J3N1
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