MolNFT v1 · #181503 · protein
Uk (B.1.1.7) SARS-cov-2 spike protein variant (S-gsas-B.1.1.7) in the 1-rbd-up conformation
7LWU · Spike glycoprotein: “Uk (B.1.1.7) SARS-cov-2 spike protein variant (S-gsas-B.1.1.7) in the 1-rbd-up conformation”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #181503 on GenesisL1: 3D…
- PDB
- 7LWU
- Type
- protein
- Length
- 2,980 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 · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 993 | 24% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 995 | 23% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 992 | 23% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 35 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 | 896 | 0.87 | 0.89 | 106 | empty |
| 2 | 1087 | 0.86 | 0.87 | 121 | empty |
| 3 | 672 | 0.81 | 0.85 | 66 | empty |
| 4 | 716 | 0.81 | 0.85 | 79 | empty |
| 5 | 209 | 0.73 | 0.88 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4688 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 4601 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 4246 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 35 glycan (disulfide, N-glycosylation).
Compared structures
- 7LWU · UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up… · 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 7LWU · PDBe 7LWU · UniProt P0DTC2
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