Research workbench
Crystal structure of dengue 2 virus envelope glycoprotein dimer in complex with the scfv fragment of the broadly neutralizing human antibody EDE1 C10
Analyse Crystal structure of dengue 2 virus envelope glycoprotein dimer in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UT9
- Type
- protein
- Length
- 2,463 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein E; Broadly neutralizing human antibody EDE1 C10
- UniProt
- Q68Y26
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein E | protein | 377 | 7% helix, 44% strand | Q68Y26 |
| B | Envelope glycoprotein E | protein | 383 | 6% helix, 49% strand | Q68Y26 |
| C | Envelope glycoprotein E | protein | 378 | 7% helix, 48% strand | Q68Y26 |
| D | Envelope glycoprotein E | protein | 380 | 5% helix, 49% strand | Q68Y26 |
| H, I, J, K | Broadly neutralizing human antibody EDE1 C10 | protein | 127 | 7% helix, 47% strand | — |
| L, M | Broadly neutralizing human antibody EDE1 C10 | protein | 110 | 0% helix, 45% strand | — |
| N | Broadly neutralizing human antibody EDE1 C10 | protein | 109 | 0% helix, 46% strand | — |
| O | Broadly neutralizing human antibody EDE1 C10 | protein | 108 | 0% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, H, B, I, C, K, D, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.81 | 0.82 | 114 | empty |
| 2 | 831 | 0.81 | 0.84 | 68 | empty |
| 3 | 637 | 0.80 | 0.85 | 65 | empty |
| 4 | 609 | 0.79 | 0.85 | 66 | empty |
| 5 | 922 | 0.77 | 0.80 | 78 | empty |
Interfaces
24 interfaces between chains.
- A–B · 1622 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1540 Ų buried · 24 hydrogen bonds · protein-protein
- J–N · 1031 Ų buried · 9 hydrogen bonds · protein-protein
- I–M · 1029 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 1026 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4UT9 · Crystal structure of dengue 2 virus envelope glycoprotein dimer in complex with the ScFv… · 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 Q68Y26
- Elsewhere: RCSB PDB 4UT9 · PDBe 4UT9 · UniProt Q68Y26
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.