Research workbench
Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody CV07-270
Analyse Crystal structure of SARS-cov-2 receptor binding domain 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
- 6XKP
- Type
- protein
- Length
- 1,253 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; CV07-270 heavy chain; CV07-270 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike protein S1 | protein | 194 | 18% helix, 29% strand | P0DTC2 |
| H | CV07-270 heavy chain | protein | 220 | 11% helix, 47% strand | — |
| L | CV07-270 light chain | protein | 211 | 6% helix, 50% strand | — |
| M | CV07-270 heavy chain | protein | 224 | 9% helix, 50% strand | — |
| N | CV07-270 light chain | protein | 210 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains H, A, L, M, B, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.75 | 0.79 | 104 | empty |
| 2 | 467 | 0.58 | 0.74 | 53 | empty |
| 3 | 55 | 0.52 | 0.87 | 18 | empty |
| 4 | 315 | 0.51 | 0.73 | 41 | empty |
| 5 | 58 | 0.47 | 0.84 | 19 | empty |
Interfaces
9 interfaces between chains.
- M–N · 1713 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1694 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 755 Ų buried · 15 hydrogen bonds · protein-protein
- B–M · 738 Ų buried · 17 hydrogen bonds · protein-protein
- B–H · 446 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6XKP · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · 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 6XKP · PDBe 6XKP · UniProt P0DTC2
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