Research workbench
Cryo-EM structure of SARS-cov-2 S-D614G variant in complex with neutralizing antibodies, rbd-CHAB15 and rbd-CHAB45
Analyse Cryo-EM structure of SARS-cov-2 S-D614G variant in complex with neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EH5
- Type
- protein
- Length
- 4,362 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Rbd-CHAB45, heavy chain; Rbd-CHAB15, light chain; Rbd-CHAB15, heavy…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 996 | 22% helix, 29% strand | P0DTC2 |
| H, I, J | Rbd-CHAB45, heavy chain | protein | 120 | 3% helix, 43% strand | — |
| O, P, Q | Rbd-CHAB15, light chain | protein | 108 | 0% helix, 46% strand | — |
| F, D, E | Rbd-CHAB15, heavy chain | protein | 120 | 5% helix, 48% strand | — |
| L, M, N | Rbd-CHAB45, light chain | protein | 110 | 0% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 75 copies · chains A, B, 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 | 985 | 0.88 | 0.90 | 111 | empty |
| 2 | 837 | 0.84 | 0.86 | 95 | empty |
| 3 | 187 | 0.79 | 0.94 | 36 | empty |
| 4 | 105 | 0.79 | 0.98 | 25 | empty |
| 5 | 143 | 0.79 | 0.95 | 31 | empty |
Interfaces
24 interfaces between chains.
- B–C · 3830 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 3817 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 3812 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 844 Ų buried · 6 hydrogen bonds · protein-protein
- J–N · 844 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7EH5 · Cryo-EM structure of SARS-CoV-2 S-D614G variant in complex with neutralizing antibodies… · the same entry in another collection · chain L against L, 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 7EH5 · PDBe 7EH5 · UniProt P0DTC2
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