Research workbench
Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibodies CV07-287 and COVA1-16
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
- 7S5R
- Type
- protein
- Length
- 1,066 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; COVA1-16 heavy chain; COVA1-16 light chain; CV07-287 heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 16 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 196 | 17% helix, 30% strand | P0DTC2 |
| H | COVA1-16 heavy chain | protein | 225 | 9% helix, 52% strand | — |
| L | COVA1-16 light chain | protein | 212 | 6% helix, 52% strand | — |
| B | CV07-287 heavy chain | protein | 219 | 3% helix, 52% strand | — |
| C | CV07-287 light chain | protein | 214 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A, L, H, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, L, H, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.64 | 0.77 | 62 | empty |
| 2 | 400 | 0.62 | 0.77 | 46 | EDO, SO4 |
| 3 | 219 | 0.56 | 0.79 | 37 | SO4 |
| 4 | 312 | 0.53 | 0.74 | 53 | empty |
| 5 | 242 | 0.53 | 0.77 | 39 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1752 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1677 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 723 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 546 Ų buried · 8 hydrogen bonds · protein-protein
- L–B · 391 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7S5R · 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 7S5R · PDBe 7S5R · UniProt P0DTC2
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