Research workbench
Cryo-EM structure of ntd-directed neutralizing antibody 4-8 Fab in complex with SARS-cov-2 S2P spike
Analyse Cryo-EM structure of ntd-directed neutralizing antibody 4-8 Fab in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LQV
- Type
- protein
- Length
- 3,980 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 4-8 heavy chain; 4-8 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1092 | 22% helix, 26% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1112 | 19% helix, 26% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1087 | 21% helix, 29% strand | P0DTC2 |
| H, W, Y | 4-8 heavy chain | protein | 125 | 2% helix, 42% strand | — |
| L, Z | 4-8 light chain | protein | 105 | 3% helix, 45% strand | — |
| X | 4-8 light chain | protein | 104 | 3% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, H, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.85 | 0.89 | 73 | empty |
| 2 | 967 | 0.85 | 0.86 | 101 | empty |
| 3 | 1175 | 0.83 | 0.84 | 133 | empty |
| 4 | 792 | 0.83 | 0.86 | 102 | empty |
| 5 | 847 | 0.82 | 0.84 | 79 | empty |
Interfaces
12 interfaces between chains.
- A–C · 5524 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 5460 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 4743 Ų buried · 38 hydrogen bonds · protein-protein
- H–L · 862 Ų buried · 8 hydrogen bonds · protein-protein
- Y–Z · 850 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7LQV · Cryo-EM structure of NTD-directed neutralizing antibody 4-8 Fab in complex with… · 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 P0DTC2
- Elsewhere: RCSB PDB 7LQV · PDBe 7LQV · UniProt P0DTC2
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