Research workbench
Chimeric flavivirus between binjari virus and dengue virus serotype-2
Analyse Chimeric flavivirus between binjari virus and dengue virus serotype-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KV8
- Type
- protein
- Length
- 1,701 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Matrix protein M
- UniProt
- A0A1X9PLJ6, A0A7D0JW86
- Ligands
- 6OU, 1Q0, NAG
- Pockets
- 18 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope protein E | protein | 493 | 22% helix, 39% strand | A0A1X9PLJ6 |
| a, c | Matrix protein M | protein | 75 | 64% helix, 0% strand | A0A7D0JW86 |
| b | Matrix protein M | protein | 72 | 64% helix, 0% strand | A0A7D0JW86 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 3 copies · chains A, B, C
- 1Q0 · (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate · ligand · 3 copies · chains A, a, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.84 | 0.85 | 122 | empty |
| 2 | 1012 | 0.75 | 0.77 | 79 | 1Q0 |
| 3 | 909 | 0.72 | 0.76 | 87 | 1Q0 |
| 4 | 716 | 0.72 | 0.78 | 66 | 1Q0 |
| 5 | 234 | 0.63 | 0.82 | 41 | empty |
Interfaces
9 interfaces between chains.
- B–b · 1726 Ų buried · 23 hydrogen bonds · protein-protein
- C–c · 1721 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1721 Ų buried · 25 hydrogen bonds · protein-protein
- A–a · 1704 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1337 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7KV8 · Chimeric flavivirus between Binjari virus and Dengue virus serotype-2 · 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 A0A1X9PLJ6
- Every structure of UniProt A0A7D0JW86
- Elsewhere: RCSB PDB 7KV8 · PDBe 7KV8 · UniProt A0A1X9PLJ6 · UniProt A0A7D0JW86
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