Research workbench
Zika specific antibody, zv-64, bound to zika envelope diii
Analyse Zika specific antibody, zv-64, 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
- 5KVF
- Type
- protein
- Length
- 546 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zika envelope diii; Zv-64 antibody Fab light chain; Zv-64 antibody Fab heavy chain
- UniProt
- A0A024B7W1
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Zika envelope diii | protein | 105 | 3% helix, 45% strand | A0A024B7W1 |
| L | Zv-64 antibody Fab light chain | protein | 220 | 6% helix, 55% strand | — |
| H | Zv-64 antibody Fab heavy chain | protein | 221 | 8% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.68 | 0.75 | 65 | GOL |
| 2 | 108 | 0.41 | 0.76 | 19 | empty |
| 3 | 124 | 0.41 | 0.75 | 25 | empty |
| 4 | 91 | 0.35 | 0.74 | 23 | empty |
| 5 | 51 | 0.32 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2046 Ų buried · 21 hydrogen bonds · protein-protein
- E–L · 542 Ų buried · 9 hydrogen bonds · protein-protein
- E–H · 366 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5KVF · Zika specific antibody, ZV-64, 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 5KVF · PDBe 5KVF · UniProt A0A024B7W1
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