Research workbench
Cryo-EM structure of south african (B.1.351) SARS-cov-2 spike glycoprotein in complex with two T6 Fab
Analyse Cryo-EM structure of south african (B.1.351) SARS-cov-2 spike glycoprotein in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FJN
- Type
- protein
- Length
- 3,418 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,ENVELOPE glycoprotein; T6 heavy chain; T6 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike GLYCOPROTEIN,ENVELOPE glycoprotein | protein | 993 | 21% helix, 31% strand | P0DTC2 |
| C | Spike GLYCOPROTEIN,ENVELOPE glycoprotein | protein | 992 | 21% helix, 31% strand | P0DTC2 |
| H, I | T6 heavy chain | protein | 107 | 0% helix, 42% strand | — |
| J, L | T6 light chain | protein | 113 | 0% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, C, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.84 | 0.89 | 63 | empty |
| 2 | 895 | 0.82 | 0.84 | 80 | empty |
| 3 | 627 | 0.82 | 0.87 | 87 | empty |
| 4 | 364 | 0.76 | 0.87 | 47 | empty |
| 5 | 520 | 0.76 | 0.84 | 58 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4633 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 4545 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 4475 Ų buried · 39 hydrogen bonds · protein-protein
- H–L · 824 Ų buried · 3 hydrogen bonds · protein-protein
- I–J · 819 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 glycan, 22 disulfide (N-glycosylation, disulfide).
Compared structures
- 7FJN · Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex… · the same entry in another collection · chain I against I, 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 7FJN · PDBe 7FJN · UniProt P0DTC2
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