Research workbench
SARS-cov-2 omicron rbd in complex with omi-25 Fab
Analyse SARS-cov-2 omicron rbd in complex with omi-25 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZFD
- Type
- protein
- Length
- 1,241 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omi-25 heavy chain; Spike protein S1; Omi-25 light chain
- UniProt
- P0DTC2
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | Omi-25 heavy chain | protein | 224 | 8% helix, 48% strand | — |
| E | Spike protein S1 | protein | 185 | 13% helix, 28% strand | P0DTC2 |
| L, B | Omi-25 light chain | protein | 213 | 5% helix, 48% strand | — |
| F | Spike protein S1 | protein | 182 | 13% helix, 31% strand | P0DTC2 |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.75 | 0.81 | 78 | empty |
| 2 | 738 | 0.67 | 0.75 | 67 | empty |
| 3 | 175 | 0.60 | 0.83 | 33 | empty |
| 4 | 393 | 0.57 | 0.75 | 48 | empty |
| 5 | 225 | 0.54 | 0.77 | 34 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1854 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1808 Ų buried · 12 hydrogen bonds · protein-protein
- F–B · 517 Ų buried · 10 hydrogen bonds · protein-protein
- E–L · 498 Ų buried · 9 hydrogen bonds · protein-protein
- H–A · 426 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7ZFD · SARS-CoV-2 Omicron RBD in complex with Omi-25 Fab · 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 7ZFD · PDBe 7ZFD · UniProt P0DTC2
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