MolNFT v1 · #191093 · protein
Omi-42 Fab in complex with SARS-cov-2 beta spike glycoprotein
7ZR7 · Spike GLYCOPROTEIN,FIBRITIN: “Omi-42 Fab in complex with SARS-cov-2 beta spike glycoprotein”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.82). MolNFT v1 #191093 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7ZR7
- Type
- protein
- Length
- 3,878 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN; Omi-42 heavy chain; Omi-42 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 1060 | 21% helix, 35% strand | P0DTC2 |
| A, C | Spike GLYCOPROTEIN,FIBRITIN | protein | 1061 | 22% helix, 35% strand | P0DTC2 |
| H, F | Omi-42 heavy chain | protein | 125 | 6% helix, 46% strand | — |
| L, E, G | Omi-42 light chain | protein | 108 | 3% helix, 49% strand | — |
| D | Omi-42 heavy chain | protein | 122 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.82 | 0.90 | 64 | empty |
| 2 | 634 | 0.80 | 0.85 | 60 | empty |
| 3 | 364 | 0.75 | 0.86 | 54 | empty |
| 4 | 685 | 0.74 | 0.80 | 53 | empty |
| 5 | 626 | 0.74 | 0.80 | 57 | empty |
Interfaces
15 interfaces between chains.
- B–C · 4075 Ų buried · 29 hydrogen bonds · protein-protein
- B–A · 4037 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 4020 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 833 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 831 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 42 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZR7 · Omi-42 Fab in complex with SARS-cov-2 beta spike glycoprotein · the same entry in another collection · chain B against B, 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 7ZR7 · PDBe 7ZR7 · UniProt P0DTC2
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