MolNFT v1 · #78829 · protein
Herpes simplex virus glycoprotein D bound to the human receptor nectin-1
3SKU: “Herpes simplex virus glycoprotein D bound to the human receptor nectin-1”. X-ray diffraction, 2 ligands (NAG, BMA), 14 pockets (best druggability 0.65). MolNFT v1 #78829 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SKU
- Type
- protein
- Length
- 1,219 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein D; Poliovirus receptor-related protein 1
- UniProt
- Q991M3, Q15223
- Ligands
- NAG, BMA
- Pockets
- 14 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein D | protein | 230 | 16% helix, 28% strand | Q991M3 |
| B | Glycoprotein D | protein | 223 | 13% helix, 29% strand | Q991M3 |
| C | Glycoprotein D | protein | 228 | 16% helix, 27% strand | Q991M3 |
| E, D | Poliovirus receptor-related protein 1 | protein | 181 | 5% helix, 48% strand | Q15223 |
| F | Poliovirus receptor-related protein 1 | protein | 176 | 2% helix, 50% strand | Q15223 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, E, D, F, B, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.65 | 0.80 | 34 | empty |
| 2 | 335 | 0.63 | 0.79 | 33 | empty |
| 3 | 323 | 0.60 | 0.78 | 32 | empty |
| 4 | 215 | 0.58 | 0.80 | 33 | empty |
| 5 | 302 | 0.54 | 0.75 | 31 | empty |
Interfaces
4 interfaces between chains.
- E–F · 1082 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 942 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 848 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 821 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
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 Q991M3
- Every structure of UniProt Q15223
- Elsewhere: RCSB PDB 3SKU · PDBe 3SKU · UniProt Q991M3 · UniProt Q15223
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