Research workbench
Crystal structure of zika virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C10
Analyse Crystal structure of zika virus envelope glycoprotein in complex with the Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A3N
- Type
- protein
- Length
- 821 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein; EDE1 C10 Fab
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- A0A1U9YHM2
- Ligands
- CA
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 395 | 8% helix, 50% strand | A0A1U9YHM2 |
| H | EDE1 C10 Fab | protein | 219 | 7% helix, 50% strand | — |
| L | EDE1 C10 Fab | protein | 207 | 7% helix, 51% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.67 | 0.77 | 45 | empty |
| 2 | 598 | 0.63 | 0.74 | 57 | empty |
| 3 | 221 | 0.60 | 0.81 | 44 | empty |
| 4 | 198 | 0.49 | 0.76 | 30 | empty |
| 5 | 88 | 0.44 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1806 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 439 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 346 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7A3N · Crystal structure of Zika virus envelope glycoprotein in complex with the Fab fragment of… · the same entry in another collection · chain A against A, 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 A0A1U9YHM2
- Elsewhere: RCSB PDB 7A3N · PDBe 7A3N · UniProt A0A1U9YHM2
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