MolNFT v1 · #174188 · protein
Open conformation of D614G SARS-cov-2 spike with 1 erect rbd
7BNN · Spike glycoprotein: “Open conformation of D614G SARS-cov-2 spike with 1 erect rbd”. Electron microscopy, 2 ligands (NAG, FUC), 20 pockets (best druggability 0.87). MolNFT v1 #174188 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7BNN
- Type
- protein
- Length
- 3,207 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 18% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1066 | 19% helix, 26% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1071 | 17% helix, 24% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1070 | 18% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 49 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · chains 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 | 1038 | 0.87 | 0.88 | 136 | empty |
| 2 | 489 | 0.84 | 0.90 | 64 | empty |
| 3 | 1019 | 0.80 | 0.81 | 83 | empty |
| 4 | 1104 | 0.79 | 0.81 | 103 | empty |
| 5 | 131 | 0.78 | 0.95 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4592 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 4459 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 4172 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 41 glycan (disulfide, N-glycosylation).
Compared structures
- 7BNN · Open conformation of D614G SARS-CoV-2 spike with 1 Erect RBD · 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 7BNN · PDBe 7BNN · UniProt P0DTC2
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