Research workbench
Crystal structure of zikv-116 Fab in complex with zikv envelope diii
Analyse Crystal structure of zikv-116 Fab in complex with zikv envelope diii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PLK
- Type
- protein
- Length
- 1,084 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zikv-116 heavy chain; Zikv-116 light chain; Env
- UniProt
- A0A1X9PPI0
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, I | Zikv-116 heavy chain | protein | 225 | 10% helix, 51% strand | — |
| L, M | Zikv-116 light chain | protein | 214 | 7% helix, 50% strand | — |
| E, F | Env | protein | 103 | 3% helix, 44% strand | A0A1X9PPI0 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.76 | 0.82 | 91 | empty |
| 2 | 140 | 0.55 | 0.82 | 36 | empty |
| 3 | 68 | 0.53 | 0.87 | 20 | empty |
| 4 | 293 | 0.53 | 0.75 | 38 | empty |
| 5 | 158 | 0.50 | 0.78 | 24 | empty |
Interfaces
9 interfaces between chains.
- I–M · 1942 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1924 Ų buried · 15 hydrogen bonds · protein-protein
- L–M · 1220 Ų buried · 15 hydrogen bonds · protein-protein
- I–F · 577 Ų buried · 12 hydrogen bonds · protein-protein
- H–E · 453 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6PLK · Crystal structure of ZIKV-116 Fab in complex with ZIKV envelope DIII · the same entry in another collection · chain L against L, 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 A0A1X9PPI0
- Elsewhere: RCSB PDB 6PLK · PDBe 6PLK · UniProt A0A1X9PPI0
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