Research workbench
Cryo-EM structure of zika virus complexed with Fab sign-3C at pH 6.5
Analyse Cryo-EM structure of zika virus complexed with Fab sign-3C at pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BU8
- Type
- protein
- Length
- 2,454 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; Zika virus M protein; Sign-3C Fab heavy chain; Sign-3C Fab light chain
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
- UniProt
- A0A024B7W1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Genome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 504 | 18% helix, 31% strand | A0A024B7W1 |
| D, E, F | Zika virus M protein | protein | 75 | 60% helix, 0% strand | — |
| G, H, J | Sign-3C Fab heavy chain | protein | 132 | 5% helix, 41% strand | — |
| I, L, K | Sign-3C Fab light chain | protein | 107 | 0% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, J, K, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.86 | 0.93 | 46 | empty |
| 2 | 993 | 0.81 | 0.83 | 112 | empty |
| 3 | 1175 | 0.80 | 0.81 | 116 | empty |
| 4 | 1022 | 0.79 | 0.81 | 96 | empty |
| 5 | 793 | 0.78 | 0.82 | 90 | empty |
Interfaces
23 interfaces between chains.
- B–E · 1847 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1845 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1827 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1622 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 1428 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7BU8 · Cryo-EM structure of zika virus complexed with Fab SIgN-3C at pH 6.5 · 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 7BU8 · PDBe 7BU8 · UniProt A0A024B7W1
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