Research workbench
Chimeric flavivirus between binjari virus and murray valley encephalitis virus
Analyse Chimeric flavivirus between binjari virus and murray valley encephalitis virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KVB
- Type
- protein
- Length
- 1,716 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Matrix protein M
- UniProt
- A0A023J5I3, A0A059ZZ36
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope protein E | protein | 501 | 21% helix, 35% strand | A0A023J5I3 |
| a, b, c | Matrix protein M | protein | 71 | 55% helix, 0% strand | A0A059ZZ36 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.81 | 0.89 | 53 | empty |
| 2 | 1148 | 0.76 | 0.78 | 107 | empty |
| 3 | 158 | 0.70 | 0.89 | 42 | empty |
| 4 | 114 | 0.63 | 0.88 | 28 | empty |
| 5 | 105 | 0.62 | 0.87 | 24 | empty |
Interfaces
9 interfaces between chains.
- B–b · 1387 Ų buried · 17 hydrogen bonds · protein-protein
- A–a · 1374 Ų buried · 16 hydrogen bonds · protein-protein
- C–c · 1372 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1336 Ų buried · 7 hydrogen bonds · protein-protein
- A–b · 903 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7KVB · Chimeric flavivirus between Binjari virus and Murray Valley encephalitis virus · 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 A0A023J5I3
- Every structure of UniProt A0A059ZZ36
- Elsewhere: RCSB PDB 7KVB · PDBe 7KVB · UniProt A0A023J5I3 · UniProt A0A059ZZ36
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