MolNFT v1 · #177050 · protein
Molecular basis for neutralizing antibody 2B11 targeting SARS-cov-2 rbd
7E5Y · Spike protein S1: “Molecular basis for neutralizing antibody 2B11 targeting SARS-cov-2 rbd”. X-ray diffraction, 10 pockets (best druggability 0.73). MolNFT v1 #177050 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E5Y
- Type
- protein
- Length
- 1,215 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; 2B11 Fab light chain; 2B11 Fab heavy chain
- UniProt
- P0DTC2
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, A | Spike protein S1 | protein | 189 | 16% helix, 27% strand | P0DTC2 |
| L | 2B11 Fab light chain | protein | 209 | 4% helix, 35% strand | — |
| H | 2B11 Fab heavy chain | protein | 206 | 3% helix, 49% strand | — |
| B | 2B11 Fab light chain | protein | 213 | 8% helix, 38% strand | — |
| C | 2B11 Fab heavy chain | protein | 209 | 7% helix, 47% strand | — |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.73 | 0.82 | 59 | empty |
| 2 | 406 | 0.70 | 0.81 | 52 | empty |
| 3 | 496 | 0.65 | 0.77 | 65 | empty |
| 4 | 472 | 0.60 | 0.74 | 46 | empty |
| 5 | 268 | 0.51 | 0.75 | 38 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1793 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1783 Ų buried · 12 hydrogen bonds · protein-protein
- R–H · 849 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 787 Ų buried · 23 hydrogen bonds · protein-protein
- L–A · 721 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7E5Y · Molecular basis for neutralizing antibody 2B11 targeting SARS-CoV-2 RBD · the same entry in another collection · chain R against R, 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 7E5Y · PDBe 7E5Y · UniProt P0DTC2
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