Research workbench
Cryo-EM structure of zika virus in complex with E protein cross- linking human monoclonal antibody ADI30056
Analyse Cryo-EM structure of zika virus in complex with E protein cross- linking human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KCR
- Type
- protein
- Length
- 1,956 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADI30056 Fab heavy chain variable region; ADI30056 Fab light chain variable region…
- UniProt
- A0A678Z1Y6
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | ADI30056 Fab heavy chain variable region | protein | 121 | 0% helix, 44% strand | — |
| L | ADI30056 Fab light chain variable region | protein | 107 | 3% helix, 44% strand | — |
| A, C, E | Envelope protein E | protein | 501 | 17% helix, 32% strand | A0A678Z1Y6 |
| B, D, F | Membrane protein M | protein | 75 | 49% helix, 0% strand | A0A678Z1Y6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.85 | 0.92 | 64 | empty |
| 2 | 1135 | 0.80 | 0.81 | 116 | empty |
| 3 | 1088 | 0.78 | 0.80 | 119 | empty |
| 4 | 705 | 0.76 | 0.81 | 65 | empty |
| 5 | 679 | 0.76 | 0.81 | 52 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1826 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1824 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1794 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1423 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 1370 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 7KCR · Cryo-EM structure of Zika virus in complex with E protein cross-linking human monoclonal… · the same entry in another collection · chain H against H, 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 A0A678Z1Y6
- Elsewhere: RCSB PDB 7KCR · PDBe 7KCR · UniProt A0A678Z1Y6
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