MolNFT v1 · #190557 · protein
The structure of ZCB11 Fab against SARS-cov-2 omicron spike
7XH8 · Spike glycoprotein: “The structure of ZCB11 Fab against SARS-cov-2 omicron spike”. Electron microscopy, 5 pockets (best druggability 0.58). MolNFT v1 #190557 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XH8
- Type
- protein
- Length
- 404 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; The heavy chain of ZCB11 antibody; The light chain of ZCB11 antibody
- UniProt
- P0DTC2
- Pockets
- 5 · best druggability 0.58
Structure
electron microscopy · 3 distinct chains · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 177 | 19% helix, 28% strand | P0DTC2 |
| B | The heavy chain of ZCB11 antibody | protein | 122 | 5% helix, 49% strand | — |
| C | The light chain of ZCB11 antibody | protein | 105 | 3% helix, 47% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.58 | 0.88 | 21 | empty |
| 2 | 168 | 0.46 | 0.76 | 19 | empty |
| 3 | 92 | 0.45 | 0.79 | 24 | empty |
| 4 | 59 | 0.35 | 0.78 | 12 | empty |
| 5 | 81 | 0.33 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 770 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 676 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 170 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7XH8 · The structure of ZCB11 Fab against SARS-CoV-2 Omicron Spike · the same entry in another collection · chain A against A, 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 7XH8 · PDBe 7XH8 · UniProt P0DTC2
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