MolNFT v1 · #172481 · protein
Crystal structure of dengue 4 virus envelope glycoprotein in complex with the scfv fragment of the broadly neutralizing human antibody EDE1 C10
7A3Q · Envelope protein E: “Crystal structure of dengue 4 virus envelope glycoprotein in complex with the scfv fragment of the broadly…”. X-ray diffraction, 2 ligands (3CX, NAG), 15 pockets (best druggability 0.79). MolNFT v1 #172481 on…
- PDB
- 7A3Q
- Type
- protein
- Length
- 1,212 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Single chain variable fragment
- UniProt
- S5S2D1
- Ligands
- 3CX, NAG
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein E | protein | 372 | 7% helix, 52% strand | S5S2D1 |
| B | Envelope protein E | protein | 366 | 8% helix, 50% strand | S5S2D1 |
| H | Single chain variable fragment | protein | 127 | 5% helix, 48% strand | — |
| I | Single chain variable fragment | protein | 126 | 5% helix, 47% strand | — |
| L | Single chain variable fragment | protein | 110 | 3% helix, 47% strand | — |
| M | Single chain variable fragment | protein | 111 | 3% helix, 47% strand | — |
Ligands and binding sites
- 3CX · (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid · ligand · 2 copies · chains H, L, I, M
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, H, B, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.79 | 0.81 | 71 | empty |
| 2 | 918 | 0.78 | 0.81 | 97 | empty |
| 3 | 955 | 0.76 | 0.79 | 94 | empty |
| 4 | 573 | 0.70 | 0.79 | 65 | empty |
| 5 | 179 | 0.50 | 0.77 | 28 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1398 Ų buried · 12 hydrogen bonds · protein-protein
- I–M · 1123 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1062 Ų buried · 12 hydrogen bonds · protein-protein
- B–M · 437 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 426 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7A3Q · Crystal structure of dengue 4 virus envelope glycoprotein 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 S5S2D1
- Elsewhere: RCSB PDB 7A3Q · PDBe 7A3Q · UniProt S5S2D1
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