Research workbench
SARS-cov-2 omicron rbd in complex with omi-32 Fab and nanobody C1
Analyse SARS-cov-2 omicron rbd in complex with omi-32 Fab and nanobody C1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZFE
- Type
- protein
- Length
- 2,948 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody C1; Spike protein S1; Omi-32 heavy chain; Omi-32 light chain
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 7 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z, X, W, Y | Nanobody C1 | protein | 124 | 7% helix, 51% strand | — |
| C | Spike protein S1 | protein | 182 | 13% helix, 27% strand | P0DTC2 |
| M, J, H, F | Omi-32 heavy chain | protein | 217 | 6% helix, 49% strand | — |
| N, K, L, G | Omi-32 light chain | protein | 216 | 6% helix, 52% strand | — |
| E | Spike protein S1 | protein | 172 | 12% helix, 27% strand | P0DTC2 |
| B | Spike protein S1 | protein | 183 | 13% helix, 27% strand | P0DTC2 |
| A | Spike protein S1 | protein | 183 | 13% helix, 27% strand | P0DTC2 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.71 | 0.98 | 24 | empty |
| 2 | 185 | 0.67 | 0.86 | 37 | empty |
| 3 | 225 | 0.67 | 0.85 | 37 | empty |
| 4 | 205 | 0.66 | 0.85 | 35 | empty |
| 5 | 246 | 0.65 | 0.83 | 36 | empty |
Interfaces
17 interfaces between chains.
- H–L · 1744 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 1736 Ų buried · 9 hydrogen bonds · protein-protein
- K–J · 1733 Ų buried · 7 hydrogen bonds · protein-protein
- M–N · 1728 Ų buried · 10 hydrogen bonds · protein-protein
- Z–E · 820 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide (disulfide).
Compared structures
- 7ZFE · SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1 · the same entry in another collection · chain Z against Z, 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 7ZFE · PDBe 7ZFE · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.