Research workbench
SARS-cov-2 S (spike glycoprotein) D614G with three (3) rbds up, bound to antibody 2-7 scfv, composite MAP
Analyse SARS-cov-2 S (spike glycoprotein) D614G with three (3) rbds up, bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T3M
- Type
- protein
- Length
- 3,771 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Antibody 2-7 scfv, variable heavy chain vh; Antibody 2-7 scfv…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Spike glycoprotein | protein | 1025 | 22% helix, 31% strand | P0DTC2 |
| D, H, I | Antibody 2-7 scfv, variable heavy chain vh | protein | 122 | 5% helix, 50% strand | — |
| J, K, L | Antibody 2-7 scfv, variable light chain vl | protein | 110 | 3% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains A, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.88 | 0.89 | 119 | empty |
| 2 | 951 | 0.87 | 0.88 | 126 | empty |
| 3 | 1191 | 0.74 | 0.77 | 105 | empty |
| 4 | 900 | 0.73 | 0.77 | 67 | empty |
| 5 | 788 | 0.73 | 0.78 | 79 | empty |
Interfaces
12 interfaces between chains.
- A–G · 4197 Ų buried · 29 hydrogen bonds · protein-protein
- C–G · 4185 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 4173 Ų buried · 28 hydrogen bonds · protein-protein
- I–K · 939 Ų buried · 6 hydrogen bonds · protein-protein
- D–L · 937 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7T3M · SARS-CoV-2 S (Spike Glycoprotein) D614G with Three (3) RBDs Up, Bound to Antibody 2-7… · 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 7T3M · PDBe 7T3M · UniProt P0DTC2
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