MolNFT v1 · #181491 · protein
Mink cluster 5-associated SARS-cov-2 spike protein (S-gsas-D614G- delfv) in the 3-rbd down conformation
7LWI · Spike glycoprotein: “Mink cluster 5-associated SARS-cov-2 spike protein (S-gsas-D614G- delfv) in the 3-rbd down conformation”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #181491 on GenesisL1…
- PDB
- 7LWI
- Type
- protein
- Length
- 3,003 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 · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1001 | 24% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 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 | 739 | 0.84 | 0.87 | 115 | empty |
| 2 | 462 | 0.81 | 0.89 | 57 | empty |
| 3 | 914 | 0.81 | 0.83 | 90 | empty |
| 4 | 593 | 0.79 | 0.85 | 62 | empty |
| 5 | 428 | 0.77 | 0.86 | 48 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5162 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 5096 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 4828 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7LWI · Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD 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 7LWI · PDBe 7LWI · UniProt P0DTC2
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