Research workbench
SARS-cov-2 omicron rbd in complex with omi-9 Fab and nanobody F2
Analyse SARS-cov-2 omicron rbd in complex with omi-9 Fab and nanobody F2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZF4
- Type
- protein
- Length
- 742 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody F2; Omi-9 heavy chain; Omi-9 light chain; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Nanobody F2 | protein | 124 | 10% helix, 47% strand | — |
| H | Omi-9 heavy chain | protein | 219 | 5% helix, 50% strand | — |
| L | Omi-9 light chain | protein | 207 | 8% helix, 48% strand | — |
| E | Spike protein S1 | protein | 192 | 17% helix, 32% strand | P0DTC2 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.71 | 0.79 | 58 | empty |
| 2 | 125 | 0.47 | 0.79 | 25 | empty |
| 3 | 58 | 0.40 | 0.81 | 21 | empty |
| 4 | 56 | 0.34 | 0.77 | 15 | empty |
| 5 | 97 | 0.33 | 0.73 | 26 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1515 Ų buried · 9 hydrogen bonds · protein-protein
- F–E · 723 Ų buried · 15 hydrogen bonds · protein-protein
- H–E · 572 Ų buried · 4 hydrogen bonds · protein-protein
- L–E · 101 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 7ZF4 · SARS-CoV-2 Omicron RBD in complex with Omi-9 Fab and nanobody F2 · the same entry in another collection · chain F against F, 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 7ZF4 · PDBe 7ZF4 · UniProt P0DTC2
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