Research workbench
Crystal structure of glycoprotein D of equine herpesvirus type 1
Analyse Crystal structure of glycoprotein D of equine herpesvirus type 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SQJ
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein D
- UniProt
- G9HV37
- Ligands
- NAG, MG
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein D | protein | 236 | 17% helix, 30% strand | G9HV37 |
| B | Glycoprotein D | protein | 236 | 17% helix, 30% strand | G9HV37 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.68 | 0.85 | 35 | empty |
| 2 | 349 | 0.66 | 0.80 | 53 | empty |
| 3 | 122 | 0.55 | 0.83 | 37 | empty |
| 4 | 124 | 0.53 | 0.82 | 31 | empty |
| 5 | 94 | 0.38 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1273 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6SQJ · Crystal structure of glycoprotein D of Equine Herpesvirus Type 1 · 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 G9HV37
- Elsewhere: RCSB PDB 6SQJ · PDBe 6SQJ · UniProt G9HV37
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.