MolNFT v1 · #177213 · protein
Cryo-EM structure of SARS-cov-2 spike D614G variant, two rbd-up conformation 2
7EB5 · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 spike D614G variant, two rbd-up conformation 2”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #177213 on GenesisL1: 3D structure, binding…
- PDB
- 7EB5
- Type
- protein
- Length
- 3,058 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 21% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 1023 | 21% helix, 26% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1011 | 21% helix, 26% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1024 | 21% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 74 copies · chains C, B, A
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 | 781 | 0.87 | 0.90 | 87 | empty |
| 2 | 1122 | 0.86 | 0.87 | 127 | empty |
| 3 | 886 | 0.82 | 0.84 | 91 | empty |
| 4 | 898 | 0.77 | 0.80 | 71 | empty |
| 5 | 843 | 0.74 | 0.79 | 83 | empty |
Interfaces
3 interfaces between chains.
- C–B · 4383 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3834 Ų buried · 28 hydrogen bonds · protein-protein
- C–A · 3665 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 35 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7EB5 · Cryo-EM structure of SARS-CoV-2 Spike D614G variant, two RBD-up conformation 2 · the same entry in another collection · chain C against C, 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 7EB5 · PDBe 7EB5 · UniProt P0DTC2
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