Research workbench
Cryo-EM structure of the zikv virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody zikv-195
Analyse Cryo-EM structure of the zikv virion in complex with Fab fragments of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MID
- Type
- protein
- Length
- 1,965 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E protein; M protein; Monoclonal antibody zikv-195 heavy chain; Monoclonal antibody…
- UniProt
- A0A024B7W1, A0A0B4J1U3
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | E protein | protein | 501 | 18% helix, 33% strand | A0A024B7W1 |
| B, D, F | M protein | protein | 75 | 48% helix, 0% strand | A0A024B7W1 |
| H | Monoclonal antibody zikv-195 heavy chain | protein | 127 | 2% helix, 31% strand | — |
| L | Monoclonal antibody zikv-195 light chain | protein | 110 | 0% helix, 39% strand | A0A0B4J1U3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, E, C, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.87 | 0.93 | 65 | empty |
| 2 | 1130 | 0.82 | 0.84 | 88 | empty |
| 3 | 1197 | 0.79 | 0.81 | 117 | empty |
| 4 | 1128 | 0.78 | 0.80 | 103 | empty |
| 5 | 752 | 0.75 | 0.80 | 66 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1733 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1731 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1720 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 1597 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1460 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6MID · Cryo-EM structure of the ZIKV virion in complex with Fab fragments of the potently… · 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 A0A0B4J1U3
- Elsewhere: RCSB PDB 6MID · PDBe 6MID · UniProt A0A024B7W1 · UniProt A0A0B4J1U3
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