Research workbench
Zika specific antibody, zv-67, bound to zika envelope diii
Analyse Zika specific antibody, zv-67, bound to zika envelope diii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KVG
- Type
- protein
- Length
- 540 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zika envelope diii; Zv-67 antibody Fab light chain; Zv-67 antibody Fab heavy chain
- UniProt
- A0A024B7W1
- Ligands
- CL
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Zika envelope diii | protein | 107 | 0% helix, 44% strand | A0A024B7W1 |
| L | Zv-67 antibody Fab light chain | protein | 214 | 5% helix, 49% strand | — |
| H | Zv-67 antibody Fab heavy chain | protein | 219 | 7% helix, 52% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.57 | 0.74 | 56 | empty |
| 2 | 169 | 0.48 | 0.76 | 29 | empty |
| 3 | 61 | 0.34 | 0.77 | 15 | empty |
| 4 | 51 | 0.32 | 0.78 | 19 | empty |
| 5 | 69 | 0.32 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1936 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 595 Ų buried · 14 hydrogen bonds · protein-protein
- E–L · 447 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5KVG · Zika specific antibody, ZV-67, bound to ZIKA envelope DIII · the same entry in another collection · chain E against E, 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 A0A024B7W1
- Elsewhere: RCSB PDB 5KVG · PDBe 5KVG · UniProt A0A024B7W1
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