MolNFT v1 · #153444 · protein
Structure of a neutralizing antibody bound to the zika envelope protein domain III
6JEP · Heavy chain of Fab ZK2B10: “Structure of a neutralizing antibody bound to the zika envelope protein domain III”. X-ray diffraction, 10 pockets (best druggability 0.66). MolNFT v1 #153444 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6JEP
- Type
- protein
- Length
- 1,100 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab ZK2B10; Light chain of Fab ZK2B10; Genome polyprotein
- UniProt
- A0A2Z2ESG6
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, K | Heavy chain of Fab ZK2B10 | protein | 235 | 9% helix, 50% strand | — |
| L, I | Light chain of Fab ZK2B10 | protein | 214 | 8% helix, 50% strand | — |
| E, F | Genome polyprotein | protein | 101 | 3% helix, 47% strand | A0A2Z2ESG6 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.66 | 0.83 | 58 | empty |
| 2 | 331 | 0.57 | 0.76 | 40 | empty |
| 3 | 298 | 0.55 | 0.76 | 42 | empty |
| 4 | 385 | 0.55 | 0.74 | 52 | empty |
| 5 | 337 | 0.53 | 0.73 | 43 | empty |
Interfaces
10 interfaces between chains.
- K–I · 1870 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1862 Ų buried · 18 hydrogen bonds · protein-protein
- H–K · 495 Ų buried · 10 hydrogen bonds · protein-protein
- H–E · 392 Ų buried · 8 hydrogen bonds · protein-protein
- K–F · 372 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6JEP · Structure of a neutralizing antibody bound to the Zika envelope protein domain III · 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 A0A2Z2ESG6
- Elsewhere: RCSB PDB 6JEP · PDBe 6JEP · UniProt A0A2Z2ESG6
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