Research workbench
SARS-cov-2 omicron BA.2 rbd in complex with covox-150 Fab (P21)
Analyse SARS-cov-2 omicron BA.2 rbd in complex with covox-150 Fab (P21) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZF9
- Type
- protein
- Length
- 1,256 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Covox-150 heavy chain; Covox-150 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Covox-150 heavy chain | protein | 220 | 10% helix, 52% strand | — |
| L, B | Covox-150 light chain | protein | 215 | 5% helix, 50% strand | — |
| E, C | Spike protein S1 | protein | 195 | 15% helix, 30% strand | P0DTC2 |
| A | Covox-150 heavy chain | protein | 216 | 10% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.56 | 0.78 | 50 | empty |
| 2 | 241 | 0.55 | 0.77 | 36 | empty |
| 3 | 364 | 0.55 | 0.74 | 45 | empty |
| 4 | 191 | 0.52 | 0.78 | 35 | empty |
| 5 | 108 | 0.50 | 0.81 | 25 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1906 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1791 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 801 Ų buried · 19 hydrogen bonds · protein-protein
- H–E · 795 Ų buried · 19 hydrogen bonds · protein-protein
- H–B · 413 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZF9 · SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab (P21) · the same entry in another collection · chain H against H, 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 7ZF9 · PDBe 7ZF9 · UniProt P0DTC2
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