Research workbench
Cryo-EM structure of dengue virus serotype 2 complexed with Fab sign- 3C at pH 6.5
Analyse Cryo-EM structure of dengue virus serotype 2 complexed with Fab sign- 3C at pH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BUB
- Type
- protein
- Length
- 2,179 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sign-3C Fab heavy chain; Sign-3C Fab light chain; Dengue virus SEROTYPE2 E protein…
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H | Sign-3C Fab heavy chain | protein | 132 | 7% helix, 42% strand | — |
| I, L | Sign-3C Fab light chain | protein | 107 | 3% helix, 47% strand | — |
| B, A, C | Dengue virus SEROTYPE2 E protein | protein | 495 | 17% helix, 27% strand | — |
| E, D, F | Dengue virus serotype 2 M protein | protein | 72 | 57% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, A, C, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.83 | 0.84 | 120 | empty |
| 2 | 486 | 0.80 | 0.87 | 80 | empty |
| 3 | 853 | 0.79 | 0.82 | 79 | empty |
| 4 | 901 | 0.77 | 0.80 | 84 | empty |
| 5 | 1036 | 0.77 | 0.79 | 113 | empty |
Interfaces
19 interfaces between chains.
- A–D · 1672 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1651 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1618 Ų buried · 12 hydrogen bonds · protein-protein
- B–A · 1325 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1263 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 7BUB · Cryo-EM structure of Dengue virus serotype 2 complexed with Fab SIgN-3C at pH 6.5 · the same entry in another collection · chain G against G, 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
- Elsewhere: RCSB PDB 7BUB · PDBe 7BUB
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