MolNFT v1 · #180029 · protein
Crystal structure of SARS-cov-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-B8 Fab
7KN3 · Spike protein S1: “Crystal structure of SARS-cov-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody…”. X-ray diffraction, 2 ligands (NAG, SO4), 11 pockets (best druggability 0.59). MolNFT v1 #180029 on…
- PDB
- 7KN3
- Type
- protein
- Length
- 1,266 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; S-B8 Fab heavy chain; S-B8 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 18% helix, 30% strand | P0DTC2 |
| B | Spike protein S1 | protein | 196 | 17% helix, 30% strand | P0DTC2 |
| H | S-B8 Fab heavy chain | protein | 219 | 9% helix, 51% strand | — |
| L, N | S-B8 Fab light chain | protein | 221 | 5% helix, 51% strand | — |
| M | S-B8 Fab heavy chain | protein | 215 | 8% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, H, L
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, H, L, M, N
- PGE · Triethylene glycol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.59 | 0.77 | 49 | empty |
| 2 | 194 | 0.54 | 0.78 | 29 | PGE |
| 3 | 216 | 0.54 | 0.77 | 39 | EDO |
| 4 | 234 | 0.51 | 0.76 | 40 | SO4 |
| 5 | 268 | 0.50 | 0.74 | 42 | empty |
Interfaces
8 interfaces between chains.
- M–N · 1784 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1782 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 807 Ų buried · 12 hydrogen bonds · protein-protein
- B–M · 764 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 347 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7KN3 · Crystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a… · 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 7KN3 · PDBe 7KN3 · UniProt P0DTC2
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