Research workbench
Complex of SARS-cov-2 spike and CR3022 Fab (non-uniform refinement)
Analyse Complex of SARS-cov-2 spike and CR3022 Fab (non-uniform refinement) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A5R
- Type
- protein
- Length
- 1,358 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CR3022 Fab heavy chain; CR3022 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.65
Structure
electron microscopy · 3 distinct chains · 5% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, I | CR3022 Fab heavy chain | protein | 213 | 1% helix, 49% strand | — |
| L, M | CR3022 Fab light chain | protein | 202 | 3% helix, 50% strand | — |
| A, B | Spike glycoprotein | protein | 264 | 9% helix, 26% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.65 | 0.87 | 37 | empty |
| 2 | 106 | 0.57 | 0.85 | 25 | empty |
| 3 | 238 | 0.53 | 0.76 | 32 | empty |
| 4 | 244 | 0.52 | 0.76 | 32 | empty |
| 5 | 136 | 0.45 | 0.77 | 22 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1669 Ų buried · 11 hydrogen bonds · protein-protein
- M–I · 1637 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 661 Ų buried · 3 hydrogen bonds · protein-protein
- B–M · 645 Ų buried · 2 hydrogen bonds · protein-protein
- B–I · 644 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7A5R · Complex of SARS-CoV-2 spike and CR3022 Fab (Non-Uniform Refinement) · the same entry in another collection · chain H against H, 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 7A5R · PDBe 7A5R · UniProt P0DTC2
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