Research workbench
Cryo-EM structure of dengue virus serotype 1 complexed with Fab fragments of human antibody 1F4
Analyse Cryo-EM structure of dengue virus serotype 1 complexed with Fab fragments of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C2I
- Type
- protein
- Length
- 2,579 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein; Polyprotein; Heavy chain Fab fragment of antibody 1F4; Light chain Fab…
- UniProt
- Q7TGE4, G3F5K5
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.46
Structure
electron microscopy · 4 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Envelope protein | protein | 495 | 0% helix, 0% strand | Q7TGE4 |
| B, D, F | Polyprotein | protein | 72 | 0% helix, 0% strand | G3F5K5 |
| H, M | Heavy chain Fab fragment of antibody 1F4 | protein | 228 | 0% helix, 0% strand | — |
| L, N | Light chain Fab fragment of antibody 1F4 | protein | 211 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains N, C, L, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.46 | 0.73 | 43 | empty |
| 2 | 50 | 0.28 | 0.73 | 19 | empty |
Interfaces
15 interfaces between chains.
- C–E · 344 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 318 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 285 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 276 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 118 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4C2I · Cryo-EM structure of Dengue virus serotype 1 complexed with Fab fragments of human… · 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 Q7TGE4
- Every structure of UniProt G3F5K5
- Elsewhere: RCSB PDB 4C2I · PDBe 4C2I · UniProt Q7TGE4 · UniProt G3F5K5
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