MolNFT v1 · #112847 · protein
HSV-1 nuclear egress complex
4ZXS · Virion egress protein UL34: “HSV-1 nuclear egress complex”. X-ray diffraction, 4 ligands (NI, ZN, NA), 7 pockets (best druggability 0.63). MolNFT v1 #112847 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZXS
- Type
- protein
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion egress protein UL34; Virion egress protein UL31
- UniProt
- P10218, P10215
- Ligands
- NI, ZN, NA, CL
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virion egress protein UL34 | protein | 159 | 21% helix, 36% strand | P10218 |
| B | Virion egress protein UL31 | protein | 242 | 45% helix, 21% strand | P10215 |
| C | Virion egress protein UL34 | protein | 161 | 20% helix, 35% strand | P10218 |
| D | Virion egress protein UL31 | protein | 241 | 46% helix, 21% strand | P10215 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
- NA · Sodium ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.63 | 0.87 | 25 | empty |
| 2 | 91 | 0.56 | 0.85 | 28 | empty |
| 3 | 148 | 0.49 | 0.78 | 22 | empty |
| 4 | 156 | 0.48 | 0.78 | 25 | empty |
| 5 | 179 | 0.48 | 0.76 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1821 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1795 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 343 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4ZXS · HSV-1 nuclear egress complex · the same entry in another collection · chain D against D, 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 P10218
- Every structure of UniProt P10215
- Elsewhere: RCSB PDB 4ZXS · PDBe 4ZXS · UniProt P10218 · UniProt P10215
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