MolNFT v1 · #187394 · protein
Crystal structure of SARS-cov-2 spike protein receptor-binding domain in complex with a highly potent antibody J08 Fab
7SBU · Spike protein S1: “Crystal structure of SARS-cov-2 spike protein receptor-binding domain in complex with a highly potent…”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.55). MolNFT v1 #187394 on GenesisL1: 3D…
- PDB
- 7SBU
- Type
- protein
- Length
- 623 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; J08 Fab heavy chain; J08 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 190 | 15% helix, 30% strand | P0DTC2 |
| H | J08 Fab heavy chain | protein | 226 | 11% helix, 50% strand | — |
| L | J08 Fab light chain | protein | 207 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.55 | 0.78 | 24 | empty |
| 2 | 356 | 0.55 | 0.74 | 43 | empty |
| 3 | 134 | 0.40 | 0.74 | 18 | empty |
| 4 | 97 | 0.36 | 0.75 | 19 | empty |
| 5 | 86 | 0.34 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1750 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 512 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 211 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7SBU · Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex 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 7SBU · PDBe 7SBU · UniProt P0DTC2
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