MolNFT v1 · #98303 · protein
Crystal structure of DENV1-E106 Fab bound to denv-1 envelope protein diii
4L5F · Heavy chain of E106 antibody (vh and CH1 of IGG2C): “Crystal structure of DENV1-E106 Fab bound to denv-1 envelope protein diii”. X-ray diffraction, 7 pockets (best druggability 0.65). MolNFT v1 #98303 on GenesisL1: 3D structure…
- PDB
- 4L5F
- Type
- protein
- Length
- 529 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of E106 antibody (vh and CH1 of IGG2C); Envelope protein; Light chain of E106…
- UniProt
- Q8BE40
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of E106 antibody (vh and CH1 of IGG2C) | protein | 218 | 7% helix, 52% strand | — |
| E | Envelope protein | protein | 98 | 0% helix, 40% strand | Q8BE40 |
| L | Light chain of E106 antibody (kappa) | protein | 213 | 7% helix, 52% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.65 | 0.75 | 65 | empty |
| 2 | 103 | 0.57 | 0.86 | 28 | empty |
| 3 | 70 | 0.32 | 0.75 | 18 | empty |
| 4 | 50 | 0.32 | 0.78 | 16 | empty |
| 5 | 83 | 0.32 | 0.73 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1987 Ų buried · 19 hydrogen bonds · protein-protein
- H–E · 487 Ų buried · 9 hydrogen bonds · protein-protein
- E–L · 231 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4L5F · Crystal Structure of DENV1-E106 Fab bound to DENV-1 Envelope protein DIII · the same entry in another collection · chain H against H, 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 Q8BE40
- Elsewhere: RCSB PDB 4L5F · PDBe 4L5F · UniProt Q8BE40
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