Research workbench
Cryoem structure of zika virus with Fab at 4.1 ångström
Analyse Cryoem structure of zika virus with Fab at 4.1 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CBP
- Type
- protein
- Length
- 2,602 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small envelope protein M; Envelope protein E; Fab heavy chain; Fab light chain
- UniProt
- A0A024B7W1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 13% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T, U, V | Small envelope protein M | protein | 75 | 49% helix, 0% strand | A0A024B7W1 |
| Q, N, K | Envelope protein E | protein | 501 | 16% helix, 33% strand | A0A024B7W1 |
| D, R | Fab heavy chain | protein | 222 | 3% helix, 28% strand | — |
| E, S | Fab light chain | protein | 215 | 5% helix, 23% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.87 | 0.94 | 60 | empty |
| 2 | 996 | 0.81 | 0.83 | 90 | empty |
| 3 | 1085 | 0.81 | 0.82 | 113 | empty |
| 4 | 891 | 0.77 | 0.80 | 90 | empty |
| 5 | 720 | 0.76 | 0.81 | 67 | empty |
Interfaces
18 interfaces between chains.
- V–Q · 1789 Ų buried · 22 hydrogen bonds · protein-protein
- U–K · 1777 Ų buried · 19 hydrogen bonds · protein-protein
- T–N · 1725 Ų buried · 17 hydrogen bonds · protein-protein
- R–S · 1718 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1686 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 2 glycan (disulfide, O-glycosylation, glycosylation).
Compared structures
- 7CBP · CryoEM structure of Zika virus with Fab at 4.1 Angstrom · the same entry in another collection · chain N against N, 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 7CBP · PDBe 7CBP · UniProt A0A024B7W1
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