Research workbench
Structure of the SARS-cov-2 rbd in complex with neutralizing antibody N-612-056
Analyse Structure of the SARS-cov-2 rbd in complex with neutralizing antibody N-612-056 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S0B
- Type
- protein
- Length
- 1,260 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-612-056 Fab heavy chain; N-612-056 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-612-056 Fab heavy chain | protein | 218 | 7% helix, 51% strand | — |
| B, D | N-612-056 light chain | protein | 213 | 7% helix, 50% strand | — |
| C | N-612-056 Fab heavy chain | protein | 219 | 7% helix, 51% strand | — |
| E | Spike protein S1 | protein | 199 | 17% helix, 29% strand | P0DTC2 |
| F | Spike protein S1 | protein | 198 | 17% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.71 | 0.78 | 82 | empty |
| 2 | 446 | 0.63 | 0.77 | 50 | empty |
| 3 | 588 | 0.62 | 0.74 | 61 | empty |
| 4 | 444 | 0.60 | 0.75 | 55 | empty |
| 5 | 521 | 0.59 | 0.74 | 62 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1905 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1838 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 632 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 578 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 551 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7S0B · Structure of the SARS-CoV-2 RBD in complex with neutralizing antibody N-612-056 · 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 7S0B · PDBe 7S0B · UniProt P0DTC2
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