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Crystal structure of the dengue virus serotype 3 envelope protein domain III in complex with the variable domains of mab 4E11
Analyse Crystal structure of the dengue virus serotype 3 envelope protein domain III in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UZE
- Type
- protein
- Length
- 623 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variable domains of murine anti-dengue mab 4E11; Envelope protein
- UniProt
- Q7TGD1
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variable domains of murine anti-dengue mab 4E11 | protein | 229 | 5% helix, 51% strand | — |
| B | Variable domains of murine anti-dengue mab 4E11 | protein | 226 | 5% helix, 51% strand | — |
| C | Envelope protein | protein | 94 | 0% helix, 45% strand | Q7TGD1 |
| D | Envelope protein | protein | 74 | 0% helix, 50% strand | Q7TGD1 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, B
- GOL · Glycerol · additive · 5 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.63 | 0.83 | 40 | GOL |
| 2 | 74 | 0.55 | 0.87 | 18 | GOL |
| 3 | 50 | 0.42 | 0.83 | 12 | EPE |
| 4 | 93 | 0.36 | 0.75 | 20 | empty |
| 5 | 64 | 0.32 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 843 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 822 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 627 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3UZE · Crystal structure of the dengue virus serotype 3 envelope protein domain III in complex… · the same entry in another collection · chain B against B, 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 Q7TGD1
- Elsewhere: RCSB PDB 3UZE · PDBe 3UZE · UniProt Q7TGD1
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