MolNFT v1 · #124983 · protein
Zika specific antibody, zv-2, bound to zika envelope diii
5KVD: “Zika specific antibody, zv-2, bound to zika envelope diii”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.47). MolNFT v1 #124983 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KVD
- Type
- protein
- Length
- 550 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zika envelope diii; Zv-2 antibody Fab light chain; Zv-2 antibody Fab heavy chain
- UniProt
- A0A024B7W1
- Ligands
- NA
- Pockets
- 7 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Zika envelope diii | protein | 108 | 8% helix, 43% strand | A0A024B7W1 |
| L | Zv-2 antibody Fab light chain | protein | 220 | 6% helix, 51% strand | — |
| H | Zv-2 antibody Fab heavy chain | protein | 222 | 8% helix, 50% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains L, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains E, H
- EDO · 1,2-ethanediol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.47 | 0.77 | 26 | empty |
| 2 | 111 | 0.45 | 0.78 | 30 | MES |
| 3 | 166 | 0.42 | 0.74 | 29 | empty |
| 4 | 102 | 0.38 | 0.75 | 23 | empty |
| 5 | 86 | 0.36 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2072 Ų buried · 18 hydrogen bonds · protein-protein
- E–H · 800 Ų buried · 17 hydrogen bonds · protein-protein
- E–L · 254 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5KVD · Zika specific antibody, ZV-2, 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 5KVD · PDBe 5KVD · UniProt A0A024B7W1
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