Research workbench
Cryo-EM structure of thermally stable zika virus strain H/PF/2013
Analyse Cryo-EM structure of thermally stable zika virus strain H/PF/2013 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IZ7
- Type
- protein
- Length
- 1,737 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein E; Structural protein M
- UniProt
- A0A024B7W1, A0A0U4DG08
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 18% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Structural protein E | protein | 504 | 14% helix, 27% strand | A0A024B7W1 |
| D, E, F | Structural protein M | protein | 75 | 44% helix, 0% strand | A0A0U4DG08 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.88 | 0.94 | 68 | empty |
| 2 | 929 | 0.78 | 0.80 | 74 | empty |
| 3 | 980 | 0.77 | 0.79 | 103 | empty |
| 4 | 652 | 0.76 | 0.81 | 62 | empty |
| 5 | 685 | 0.73 | 0.79 | 57 | empty |
Interfaces
9 interfaces between chains.
- B–E · 1811 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1785 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1714 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1454 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 1452 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5IZ7 · Cryo-EM structure of thermally stable Zika virus strain H/PF/2013 · 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
- Every structure of UniProt A0A0U4DG08
- Elsewhere: RCSB PDB 5IZ7 · PDBe 5IZ7 · UniProt A0A024B7W1 · UniProt A0A0U4DG08
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