MolNFT v1 · #72284 · protein
Crystal structure of the immature envelope glycoprotein complex of chikungunya virus.
3N40 · P62 envelope glycoprotein: “Crystal structure of the immature envelope glycoprotein complex of chikungunya virus.”. X-ray diffraction, 2 ligands (NAG, NDG), 13 pockets (best druggability 0.74). MolNFT v1 #72284 on GenesisL1: 3D…
- PDB
- 3N40
- Type
- protein
- Length
- 794 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P62 envelope glycoprotein; E1 envelope glycoprotein
- UniProt
- Q1H8W5
- Ligands
- NAG, NDG
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | P62 envelope glycoprotein | protein | 401 | 8% helix, 45% strand | Q1H8W5 |
| F | E1 envelope glycoprotein | protein | 393 | 6% helix, 50% strand | Q1H8W5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains P, F
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains F
- ACT · Acetate ion · additive · 5 copies · chains P, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.74 | 0.82 | 57 | empty |
| 2 | 457 | 0.73 | 0.83 | 51 | empty |
| 3 | 86 | 0.66 | 0.91 | 27 | empty |
| 4 | 190 | 0.57 | 0.80 | 21 | empty |
| 5 | 129 | 0.54 | 0.82 | 23 | empty |
Interfaces
1 interface between chains.
- P–F · 2515 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3N40 · Crystal structure of the immature envelope glycoprotein complex of Chikungunya virus. · the same entry in another collection · chain P against P, 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 Q1H8W5
- Elsewhere: RCSB PDB 3N40 · PDBe 3N40 · UniProt Q1H8W5
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