MolNFT v1 · #177457 · protein
Cryo-EM structure of SARS-cov-2 spike in complex with a neutralizing antibody rbd-chab-25
7EJ4 · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 spike in complex with a neutralizing antibody rbd-chab-25”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #177457 on GenesisL1: 3D structure…
- PDB
- 7EJ4
- Type
- protein
- Length
- 3,725 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Rbd-chab-25, heavy chain; Rbd-chab-25, light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1008 | 21% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1022 | 23% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1011 | 22% helix, 29% strand | P0DTC2 |
| H, I, J | Rbd-chab-25, heavy chain | protein | 119 | 5% helix, 34% strand | — |
| L, M, N | Rbd-chab-25, light chain | protein | 109 | 3% helix, 35% 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 | 625 | 0.86 | 0.91 | 74 | empty |
| 2 | 520 | 0.79 | 0.86 | 58 | empty |
| 3 | 507 | 0.77 | 0.84 | 49 | empty |
| 4 | 762 | 0.76 | 0.80 | 55 | empty |
| 5 | 446 | 0.75 | 0.84 | 49 | empty |
Interfaces
13 interfaces between chains.
- B–C · 3859 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 3822 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 3748 Ų buried · 31 hydrogen bonds · protein-protein
- J–N · 884 Ų buried · 5 hydrogen bonds · protein-protein
- I–M · 868 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 43 disulfide (N-glycosylation, disulfide).
Compared structures
- 7EJ4 · Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-25 · the same entry in another collection · chain M against M, 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 7EJ4 · PDBe 7EJ4 · UniProt P0DTC2
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