MolNFT v1 · #174404 · protein
Cryo-EM structure of dengue virus serotype 2 complexed with Fab sign- 3C at pH 8.0
7BUD · Sign-3C Fab heavy chain: “Cryo-EM structure of dengue virus serotype 2 complexed with Fab sign- 3C at pH 8.0”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #174404 on GenesisL1: 3D structure…
- PDB
- 7BUD
- 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 serotype 2 E protein…
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 17% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H | Sign-3C Fab heavy chain | protein | 132 | 2% helix, 41% strand | — |
| I, L | Sign-3C Fab light chain | protein | 107 | 3% helix, 49% strand | — |
| B, A, C | Dengue virus serotype 2 E protein | protein | 495 | 18% helix, 25% strand | — |
| E, D, F | Dengue virus serotype 2 M protein | protein | 72 | 56% 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.83 | 0.89 | 79 | empty |
| 2 | 1146 | 0.83 | 0.84 | 115 | empty |
| 3 | 453 | 0.83 | 0.90 | 70 | empty |
| 4 | 976 | 0.79 | 0.81 | 84 | empty |
| 5 | 994 | 0.79 | 0.80 | 106 | empty |
Interfaces
18 interfaces between chains.
- C–F · 1605 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1525 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1516 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1307 Ų buried · 4 hydrogen bonds · protein-protein
- B–A · 1233 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 7BUD · Cryo-EM structure of Dengue virus serotype 2 complexed with Fab SIgN-3C at pH 8.0 · 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
- Elsewhere: RCSB PDB 7BUD · PDBe 7BUD
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