MolNFT v1 · #85755 · protein
Structure of dengue virus strain 4 diii in complex with Fab 2H12
4AM0 · Fab 2H12, heavy chain: “Structure of dengue virus strain 4 diii in complex with Fab 2H12”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #85755 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4AM0
- Type
- protein
- Length
- 2,070 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 2H12, heavy chain; Fab 2H12, light chain; Envelope protein,
- UniProt
- Q7TGC6
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fab 2H12, heavy chain | protein | 211 | 7% helix, 51% strand | — |
| B, D, F, L | Fab 2H12, light chain | protein | 212 | 6% helix, 51% strand | — |
| E | Fab 2H12, heavy chain | protein | 212 | 7% helix, 50% strand | — |
| H | Fab 2H12, heavy chain | protein | 214 | 7% helix, 50% strand | — |
| Q | Envelope protein, | protein | 91 | 3% helix, 48% strand | Q7TGC6 |
| R | Envelope protein, | protein | 96 | 3% helix, 47% strand | Q7TGC6 |
| S | Envelope protein, | protein | 92 | 3% helix, 48% strand | Q7TGC6 |
| T | Envelope protein, | protein | 95 | 3% helix, 51% strand | Q7TGC6 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.80 | 0.83 | 104 | empty |
| 2 | 612 | 0.77 | 0.83 | 81 | empty |
| 3 | 218 | 0.56 | 0.79 | 33 | empty |
| 4 | 175 | 0.56 | 0.80 | 35 | empty |
| 5 | 238 | 0.53 | 0.77 | 35 | empty |
Interfaces
28 interfaces between chains.
- E–F · 1749 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1746 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1741 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1734 Ų buried · 19 hydrogen bonds · protein-protein
- E–Q · 327 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4AM0 · Structure of Dengue virus strain 4 DIII in complex with Fab 2H12 · 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 Q7TGC6
- Elsewhere: RCSB PDB 4AM0 · PDBe 4AM0 · UniProt Q7TGC6
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