Research workbench
Omi-2 Fab in complex with SARS-cov-2 beta spike glycoprotein
Analyse Omi-2 Fab in complex with SARS-cov-2 beta spike glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZR9
- Type
- protein
- Length
- 3,899 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN; Omi-2 Fab heavy chain; Omi-2 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 1060 | 21% helix, 34% strand | P0DTC2 |
| A, C | Spike GLYCOPROTEIN,FIBRITIN | protein | 1061 | 21% helix, 34% strand | P0DTC2 |
| H, D, F | Omi-2 Fab heavy chain | protein | 131 | 9% helix, 41% strand | — |
| L, E, G | Omi-2 Fab light chain | protein | 108 | 6% helix, 55% 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 | 879 | 0.85 | 0.87 | 114 | empty |
| 2 | 804 | 0.82 | 0.85 | 86 | empty |
| 3 | 576 | 0.81 | 0.87 | 62 | empty |
| 4 | 277 | 0.75 | 0.88 | 42 | empty |
| 5 | 623 | 0.75 | 0.81 | 59 | empty |
Interfaces
13 interfaces between chains.
- A–C · 4356 Ų buried · 27 hydrogen bonds · protein-protein
- B–A · 4177 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4108 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 839 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 836 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 42 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZR9 · Omi-2 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 7ZR9 · PDBe 7ZR9 · UniProt P0DTC2
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