Research workbench
Crystal structure of the SARS-cov-2 rbd in complex with the human antibody CV2.6264
Analyse Crystal structure of the SARS-cov-2 rbd in complex with the human antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QF1
- Type
- protein
- Length
- 1,248 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; CV2.6264 light chain; CV2.6264 heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 15% helix, 29% strand | P0DTC2 |
| F | Spike protein S1 | protein | 190 | 16% helix, 29% strand | P0DTC2 |
| B, D | CV2.6264 light chain | protein | 213 | 7% helix, 50% strand | — |
| C | CV2.6264 heavy chain | protein | 219 | 5% helix, 51% strand | — |
| E | CV2.6264 heavy chain | protein | 219 | 7% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D, F, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.83 | 0.84 | 95 | empty |
| 2 | 435 | 0.58 | 0.74 | 47 | empty |
| 3 | 414 | 0.58 | 0.75 | 48 | empty |
| 4 | 259 | 0.51 | 0.75 | 30 | empty |
| 5 | 192 | 0.46 | 0.75 | 36 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1723 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1695 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 635 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 582 Ų buried · 10 hydrogen bonds · protein-protein
- F–E · 546 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7QF1 · Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.6264 · the same entry in another collection · chain E against E, 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 7QF1 · PDBe 7QF1 · UniProt P0DTC2
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