Research workbench
The interface of JMB2002 Fab binds to SARS-cov-2 omicron variant S
Analyse The interface of JMB2002 Fab binds to SARS-cov-2 omicron variant S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WRV
- Type
- protein
- Length
- 427 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; JMB2002 Fab heavy chain; JMB2002 Fab light chain
- UniProt
- P0DTC2
- Pockets
- 4 · best druggability 0.45
Structure
electron microscopy · 3 distinct chains · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 199 | 17% helix, 26% strand | P0DTC2 |
| U | JMB2002 Fab heavy chain | protein | 122 | 5% helix, 49% strand | — |
| V | JMB2002 Fab light chain | protein | 106 | 3% helix, 52% strand | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.45 | 0.77 | 20 | empty |
| 2 | 115 | 0.39 | 0.75 | 18 | empty |
| 3 | 70 | 0.34 | 0.76 | 18 | empty |
| 4 | 53 | 0.29 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- U–V · 828 Ų buried · 5 hydrogen bonds · protein-protein
- C–U · 692 Ų buried · 13 hydrogen bonds · protein-protein
- C–V · 429 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7WRV · The interface of JMB2002 Fab binds to SARS-CoV-2 Omicron Variant S · the same entry in another collection · chain C against C, 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 7WRV · PDBe 7WRV · UniProt P0DTC2
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