MolNFT v1 · #11424 · protein
Crystal structure of the herpes simplex virus glycoprotein D bound to the cellular receptor HVEA/HVEM
1JMA · Herpesvirus entry mediator: “Crystal structure of the herpes simplex virus glycoprotein D bound to the cellular receptor HVEA/HVEM”. X-ray diffraction, 2 ligands (NAG, SO4), 3 pockets (best druggability 0.39). MolNFT v1 #11424 on…
- PDB
- 1JMA
- Type
- protein
- Length
- 359 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Herpesvirus entry mediator; Glycoprotein D
- UniProt
- Q92956, P57083
- Ligands
- NAG, SO4
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Herpesvirus entry mediator | protein | 100 | 0% helix, 37% strand | Q92956 |
| A | Glycoprotein D | protein | 259 | 16% helix, 31% strand | P57083 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.39 | 0.75 | 26 | SO4 |
| 2 | 55 | 0.35 | 0.78 | 22 | empty |
| 3 | 74 | 0.35 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- B–A · 823 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1JMA · Crystal structure of the herpes simplex virus glycoprotein D bound to the cellular… · the same entry in another collection · chain B against B, TM-score 1.00
- Q92956 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain B against A, TM-score 0.88
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 Q92956
- Every structure of UniProt P57083
- Elsewhere: RCSB PDB 1JMA · PDBe 1JMA · UniProt Q92956 · UniProt P57083
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