Research workbench
Electron cryo-microscopy of chikungunya vlp in complex with mouse MXRA8 receptor
Analyse Electron cryo-microscopy of chikungunya vlp in complex with mouse MXRA8 receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NK6
- Type
- protein
- Length
- 5,104 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix remodeling-associated protein 8; E1 glycoprotein; E2 glycoprotein; Capsid protein
- UniProt
- Q9DBV4, Q5XXP3
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 5 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, O, P | Matrix remodeling-associated protein 8 | protein | 269 | 11% helix, 43% strand | Q9DBV4 |
| N | Matrix remodeling-associated protein 8 | protein | 261 | 10% helix, 44% strand | Q9DBV4 |
| A, B, C, D | E1 glycoprotein | protein | 439 | 10% helix, 44% strand | Q5XXP3 |
| E, F, G, H | E2 glycoprotein | protein | 419 | 8% helix, 35% strand | Q5XXP3 |
| I, J, K, L | Capsid protein | protein | 151 | 7% helix, 50% strand | Q5XXP3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains M, N, O, P, A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.89 | 0.90 | 115 | empty |
| 2 | 923 | 0.88 | 0.90 | 114 | empty |
| 3 | 803 | 0.88 | 0.91 | 108 | empty |
| 4 | 1180 | 0.86 | 0.87 | 120 | empty |
| 5 | 1075 | 0.86 | 0.87 | 105 | empty |
Interfaces
42 interfaces between chains.
- C–G · 3297 Ų buried · 30 hydrogen bonds · protein-protein
- D–H · 3286 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 3235 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 3185 Ų buried · 23 hydrogen bonds · protein-protein
- O–E · 1050 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6NK6 · Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor · the same entry in another collection · chain L against L, 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 Q9DBV4
- Every structure of UniProt Q5XXP3
- Elsewhere: RCSB PDB 6NK6 · PDBe 6NK6 · UniProt Q9DBV4 · UniProt Q5XXP3
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