MolNFT v1 · #172478 · protein
Crystal structure of zika virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C10
7A3N · Core protein: “Crystal structure of zika virus envelope glycoprotein in complex with the Fab fragment of the broadly…”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.67). MolNFT v1 #172478 on GenesisL1: 3D…
- 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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