Research workbench
Cryo-EM structure of zika virus complexed with Fab C10 at pH 8.0
Analyse Cryo-EM structure of zika virus complexed with Fab C10 at pH 8.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H37
- Type
- protein
- Length
- 2,425 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein E; Strutural protein M; C10 IgG heavy chain variable region; C10 IgG…
- UniProt
- A0A024B7W1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 16% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural protein E | protein | 504 | 18% helix, 25% strand | A0A024B7W1 |
| C, B | Structural protein E | protein | 494 | 15% helix, 16% strand | A0A024B7W1 |
| D, E, F | Strutural protein M | protein | 75 | 59% helix, 0% strand | A0A024B7W1 |
| G, K, I | C10 IgG heavy chain variable region | protein | 127 | 0% helix, 33% strand | — |
| H, L, M | C10 IgG light chain variable region | protein | 109 | 5% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.87 | 0.92 | 75 | empty |
| 2 | 1104 | 0.85 | 0.86 | 113 | empty |
| 3 | 1157 | 0.84 | 0.85 | 126 | empty |
| 4 | 414 | 0.77 | 0.86 | 54 | empty |
| 5 | 496 | 0.76 | 0.85 | 84 | empty |
Interfaces
24 interfaces between chains.
- C–F · 1819 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1803 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 1697 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1561 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1367 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5H37 · Cryo-EM structure of zika virus complexed with Fab C10 at pH 8.0 · 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 A0A024B7W1
- Elsewhere: RCSB PDB 5H37 · PDBe 5H37 · UniProt A0A024B7W1
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