Research workbench
Crystal structure of L107C/A313C covalently linked dengue 2 virus envelope glycoprotein dimer in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 A11
Analyse Crystal structure of L107C/A313C covalently linked dengue 2 virus envelope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N09
- Type
- protein
- Length
- 1,657 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein E; Broadly neutralizing human antibody EDE2 A11 - heavy chain…
- UniProt
- C3VXD1
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein E | protein | 391 | 6% helix, 50% strand | C3VXD1 |
| B | Envelope glycoprotein E | protein | 388 | 7% helix, 49% strand | C3VXD1 |
| H, I | Broadly neutralizing human antibody EDE2 A11 - heavy chain | protein | 226 | 9% helix, 49% strand | — |
| L, M | Broadly neutralizing human antibody EDE2 A11 - light chain | protein | 213 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, I, H
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains I, M, H, L
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains I, M, H, L
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.77 | 0.79 | 109 | empty |
| 2 | 727 | 0.73 | 0.79 | 64 | empty |
| 3 | 667 | 0.69 | 0.77 | 61 | empty |
| 4 | 621 | 0.66 | 0.76 | 67 | empty |
| 5 | 568 | 0.63 | 0.75 | 62 | empty |
Interfaces
12 interfaces between chains.
- I–M · 2048 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 2014 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1855 Ų buried · 24 hydrogen bonds · protein-protein
- A–H · 594 Ų buried · 14 hydrogen bonds · protein-protein
- B–I · 549 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5N09 · Crystal structure of L107C/A313C covalently linked dengue 2 virus envelope glycoprotein… · 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 C3VXD1
- Elsewhere: RCSB PDB 5N09 · PDBe 5N09 · UniProt C3VXD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.