MolNFT v1 · #177194 · protein
Immune complex of SARS-cov-2 rbd and cross-neutralizing antibody 7D6
7EAM · Spike protein S1: “Immune complex of SARS-cov-2 rbd and cross-neutralizing antibody 7D6”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.66). MolNFT v1 #177194 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7EAM
- Type
- protein
- Length
- 1,266 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; The heavy chain of Fab fragment of antibody 7D6; The light chain of Fab…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike protein S1 | protein | 204 | 15% helix, 29% strand | P0DTC2 |
| H, C | The heavy chain of Fab fragment of antibody 7D6 | protein | 215 | 7% helix, 52% strand | — |
| L, D | The light chain of Fab fragment of antibody 7D6 | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.66 | 0.79 | 32 | empty |
| 2 | 448 | 0.64 | 0.78 | 51 | empty |
| 3 | 364 | 0.64 | 0.79 | 32 | empty |
| 4 | 610 | 0.63 | 0.75 | 77 | empty |
| 5 | 396 | 0.63 | 0.78 | 40 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1854 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1849 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 662 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 660 Ų buried · 12 hydrogen bonds · protein-protein
- L–C · 387 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7EAM · immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6 · 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 7EAM · PDBe 7EAM · UniProt P0DTC2
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