Research workbench
Cryo-EM structure of zika virus complexed with Fab of ZKA190 at pH 8.0 and 37 celsius degree
Analyse Cryo-EM structure of zika virus complexed with Fab of ZKA190 at pH 8.0 and 37… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y0A
- Type
- protein
- Length
- 1,875 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein E; Variable region of Fab ZKA190 heavy chain; Variable region of Fab ZKA190 light…
- UniProt
- A0A1V0E2E9
- Pockets
- 6 · best druggability 0.42
Structure
electron microscopy · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Protein E | protein | 388 | 0% helix, 0% strand | A0A1V0E2E9 |
| H, F, D | Variable region of Fab ZKA190 heavy chain | protein | 129 | 0% helix, 0% strand | — |
| L, G, E | Variable region of Fab ZKA190 light chain | protein | 108 | 0% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.42 | 0.73 | 37 | empty |
| 2 | 108 | 0.40 | 0.74 | 30 | empty |
| 3 | 87 | 0.33 | 0.72 | 26 | empty |
| 4 | 72 | 0.31 | 0.72 | 27 | empty |
| 5 | 55 | 0.28 | 0.72 | 20 | empty |
Interfaces
10 interfaces between chains.
- A–B · 251 Ų buried · 0 hydrogen bonds · protein-protein
- B–G · 187 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 167 Ų buried · 0 hydrogen bonds · protein-protein
- C–L · 102 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 77 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Y0A · Cryo-EM structure of zika virus complexed with Fab of ZKA190 at pH 8.0 and 37 celsius… · 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 A0A1V0E2E9
- Elsewhere: RCSB PDB 5Y0A · PDBe 5Y0A · UniProt A0A1V0E2E9
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