MolNFT v1 · #93120 · protein
Structure of dengue virus serotype 1 se containing stem to residue 421
4GT0 · Envelope protein E: “Structure of dengue virus serotype 1 se containing stem to residue 421”. X-ray diffraction, 3 ligands (NAG, CD, CL), 6 pockets (best druggability 0.75). MolNFT v1 #93120 on GenesisL1: 3D structure, binding sites…
- PDB
- 4GT0
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E
- UniProt
- P17763
- Ligands
- NAG, CD, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein E | protein | 390 | 8% helix, 51% strand | P17763 |
| B | Envelope protein E | protein | 390 | 6% helix, 51% strand | P17763 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.75 | 0.80 | 78 | empty |
| 2 | 704 | 0.74 | 0.80 | 79 | CD |
| 3 | 135 | 0.48 | 0.78 | 20 | CD |
| 4 | 78 | 0.39 | 0.78 | 20 | CD |
| 5 | 123 | 0.36 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 271 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4GT0 · Structure of dengue virus serotype 1 sE containing stem to residue 421 · 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 P17763
- Elsewhere: RCSB PDB 4GT0 · PDBe 4GT0 · UniProt P17763
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