MolNFT v1 · #190518 · protein
Cryo-EM structure of SARS-cov-2 omicron rbd in complex with S309 Fab (local refinement)
7XCK · S309 heavy chain: “Cryo-EM structure of SARS-cov-2 omicron rbd in complex with S309 Fab (local refinement)”. Electron microscopy, 2 ligands (NAG, FUC), 8 pockets (best druggability 0.58). MolNFT v1 #190518 on GenesisL1: 3D…
- PDB
- 7XCK
- Type
- protein
- Length
- 704 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S309 heavy chain; S309 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 8 · best druggability 0.58
Structure
electron microscopy · 3 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S309 heavy chain | protein | 223 | 4% helix, 47% strand | — |
| B | S309 light chain | protein | 212 | 5% helix, 48% strand | — |
| M | Spike protein S1 | protein | 269 | 10% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, M
- FUC · alpha-L-fucopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.58 | 0.74 | 56 | NAG, FUC |
| 2 | 236 | 0.56 | 0.78 | 34 | empty |
| 3 | 173 | 0.55 | 0.80 | 25 | empty |
| 4 | 72 | 0.52 | 0.85 | 18 | empty |
| 5 | 240 | 0.47 | 0.73 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1585 Ų buried · 5 hydrogen bonds · protein-protein
- A–M · 696 Ų buried · 11 hydrogen bonds · protein-protein
- B–M · 157 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7XCK · Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement) · 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 7XCK · PDBe 7XCK · UniProt P0DTC2
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