MolNFT v1 · #169756 · protein
Structure of SARS-cov-2 spike at pH 5.5, all rbds down
6XM5 · Spike glycoprotein: “Structure of SARS-cov-2 spike at pH 5.5, all rbds down”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #169756 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XM5
- Type
- protein
- Length
- 3,149 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 0.84
Structure
electron microscopy · 3 distinct chains · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1057 | 20% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1056 | 21% helix, 27% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1036 | 19% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 58 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 | 507 | 0.84 | 0.91 | 58 | empty |
| 2 | 928 | 0.84 | 0.85 | 105 | empty |
| 3 | 876 | 0.84 | 0.86 | 112 | empty |
| 4 | 987 | 0.82 | 0.83 | 84 | empty |
| 5 | 768 | 0.82 | 0.85 | 98 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6055 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 5614 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 4950 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 glycan, 41 disulfide (N-glycosylation, disulfide).
Compared structures
- 6XM5 · Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down · 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 6XM5 · PDBe 6XM5 · UniProt P0DTC2
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