Research workbench
Cryo-EM structure of ntd-directed neutralizing antibody LP5 Fab in complex with SARS-cov-2 S2P spike
Analyse Cryo-EM structure of ntd-directed neutralizing antibody LP5 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
- 7MXP
- Type
- protein
- Length
- 3,967 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; LP5 Fab heavy chain; LP5 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 17% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1098 | 18% helix, 27% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1101 | 19% helix, 26% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1090 | 19% helix, 28% strand | P0DTC2 |
| G, I, H | LP5 Fab heavy chain | protein | 119 | 0% helix, 28% strand | — |
| J, K, L | LP5 Fab light chain | protein | 107 | 3% helix, 15% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 48 copies · chains B, G, A, I, C, H
- BMA · beta-D-mannopyranose · sugar · 7 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains G, I, H
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B, G, A, I, C, H
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 | 1042 | 0.88 | 0.89 | 140 | empty |
| 2 | 528 | 0.83 | 0.89 | 64 | empty |
| 3 | 877 | 0.82 | 0.84 | 104 | empty |
| 4 | 161 | 0.82 | 0.97 | 38 | empty |
| 5 | 769 | 0.81 | 0.85 | 105 | empty |
Interfaces
12 interfaces between chains.
- A–B · 5305 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 4938 Ų buried · 59 hydrogen bonds · protein-protein
- B–C · 4886 Ų buried · 46 hydrogen bonds · protein-protein
- G–J · 1144 Ų buried · 12 hydrogen bonds · protein-protein
- I–K · 979 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 7MXP · Cryo-EM structure of NTD-directed neutralizing antibody LP5 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 7MXP · PDBe 7MXP · UniProt P0DTC2
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