Research workbench
2C8 Fab bound to ediii of denv 2
Analyse 2C8 Fab bound to ediii of denv 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FLC
- Type
- protein
- Length
- 1,050 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of 2C8 Fab; Heavy chain of 2C8 Fab; Domain III of dengue virus 2
- UniProt
- P14340
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light chain of 2C8 Fab | protein | 211 | 5% helix, 52% strand | — |
| B, H | Heavy chain of 2C8 Fab | protein | 216 | 7% helix, 53% strand | — |
| G | Domain III of dengue virus 2 | protein | 98 | 0% helix, 46% strand | P14340 |
| I | Domain III of dengue virus 2 | protein | 97 | 0% helix, 44% strand | P14340 |
| L | Light chain of 2C8 Fab | protein | 212 | 5% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.69 | 0.77 | 74 | empty |
| 2 | 779 | 0.69 | 0.76 | 80 | empty |
| 3 | 209 | 0.52 | 0.77 | 33 | GOL |
| 4 | 138 | 0.43 | 0.76 | 22 | empty |
| 5 | 110 | 0.42 | 0.77 | 20 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1920 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1912 Ų buried · 20 hydrogen bonds · protein-protein
- A–I · 445 Ų buried · 11 hydrogen bonds · protein-protein
- G–L · 439 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 409 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6FLC · 2C8 Fab bound to EDIII of DenV 2 · 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 P14340
- Elsewhere: RCSB PDB 6FLC · PDBe 6FLC · UniProt P14340
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