Research workbench
Electron cryo-microscopy of chikungunya in complex with mouse MXRA8 receptor
Analyse Electron cryo-microscopy of chikungunya 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
- 6NK7
- Type
- protein
- Length
- 4,537 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E1 glycoprotein; E2 glycoprotein; Capsid protein; E3 glycoprotein; Matrix…
- EC
- 3.4.21.90
- UniProt
- Q88628, D2KBQ2, Q9DBV4
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 9% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | E1 glycoprotein (EC 3.4.21.90) | protein | 439 | 8% helix, 39% strand | Q88628 |
| E, F, G, H | E2 glycoprotein (EC 3.4.21.90) | protein | 419 | 7% helix, 32% strand | Q88628 |
| I, J, K, L | Capsid protein (EC 3.4.21.90) | protein | 151 | 2% helix, 36% strand | Q88628 |
| U, V, W, X | E3 glycoprotein (EC 3.4.21.90) | protein | 60 | 37% helix, 10% strand | D2KBQ2 |
| N | Matrix remodeling-associated protein 8 | protein | 261 | 10% helix, 44% strand | Q9DBV4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D, N
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 | 627 | 0.86 | 0.91 | 81 | empty |
| 2 | 1010 | 0.86 | 0.87 | 105 | empty |
| 3 | 948 | 0.85 | 0.86 | 112 | empty |
| 4 | 1138 | 0.84 | 0.84 | 88 | empty |
| 5 | 187 | 0.82 | 0.96 | 42 | empty |
Interfaces
32 interfaces between chains.
- C–G · 3215 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 3183 Ų buried · 32 hydrogen bonds · protein-protein
- D–H · 3146 Ų buried · 39 hydrogen bonds · protein-protein
- B–F · 3062 Ų buried · 38 hydrogen bonds · protein-protein
- H–U · 952 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide, 9 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6NK7 · Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor · the same entry in another collection · chain N against N, 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 Q88628
- Every structure of UniProt D2KBQ2
- Every structure of UniProt Q9DBV4
- Elsewhere: RCSB PDB 6NK7 · PDBe 6NK7 · UniProt Q88628 · UniProt D2KBQ2 · UniProt Q9DBV4
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