Research workbench
Omi-38 Fab in complex with SARS-cov-2 beta spike rbd (local refinement)
Analyse Omi-38 Fab in complex with SARS-cov-2 beta spike rbd (local refinement) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZR8
- Type
- protein
- Length
- 471 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN; Omi-38 Fab heavy chain; Omi-38 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.55
Structure
electron microscopy · 3 distinct chains · 7% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 245 | 11% helix, 29% strand | P0DTC2 |
| H | Omi-38 Fab heavy chain | protein | 118 | 3% helix, 54% strand | — |
| L | Omi-38 Fab light chain | protein | 108 | 3% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 172 | 0.55 | 0.80 | 27 | empty |
| 2 | 109 | 0.37 | 0.74 | 23 | empty |
| 3 | 64 | 0.29 | 0.74 | 12 | empty |
| 4 | 53 | 0.27 | 0.74 | 15 | empty |
| 5 | 50 | 0.25 | 0.73 | 11 | empty |
Interfaces
3 interfaces between chains.
- H–L · 874 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 593 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 448 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZR8 · OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE RBD (local refinement) · 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 7ZR8 · PDBe 7ZR8 · UniProt P0DTC2
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