MolNFT v1 · #156429 · protein
Post-fusion structure of SARS-cov spike glycoprotein
6M3W: “Post-fusion structure of SARS-cov spike glycoprotein”. Electron microscopy, 1 ligand (NAG), 11 pockets (best druggability 0.82). MolNFT v1 #156429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6M3W
- Type
- protein
- Length
- 1,032 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P59594
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 344 | 47% helix, 17% strand | P59594 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.82 | 0.83 | 101 | empty |
| 2 | 319 | 0.80 | 0.91 | 45 | empty |
| 3 | 66 | 0.74 | 0.98 | 12 | empty |
| 4 | 116 | 0.71 | 0.93 | 23 | empty |
| 5 | 234 | 0.66 | 0.83 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6423 Ų buried · 86 hydrogen bonds · protein-protein
- A–B · 6399 Ų buried · 82 hydrogen bonds · protein-protein
- B–C · 6363 Ų buried · 78 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 6M3W · Post-fusion structure of SARS-CoV spike glycoprotein · the same entry in another collection · chain B against B, TM-score 1.00
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.16
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.16
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain B against E, TM-score 0.15
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain B against E, TM-score 0.15
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 P59594
- Elsewhere: RCSB PDB 6M3W · PDBe 6M3W · UniProt P59594
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