Research workbench
Mink cluster 5-associated SARS-cov-2 spike protein (S-gsas-D614G- delfv) in the 1-rbd up conformation
Analyse Mink cluster 5-associated SARS-cov-2 spike protein (S-gsas-D614G- delfv) in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LWM
- 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 | 23% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 995 | 24% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 992 | 23% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 37 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 | 1190 | 0.87 | 0.88 | 141 | empty |
| 2 | 950 | 0.87 | 0.88 | 114 | empty |
| 3 | 731 | 0.79 | 0.83 | 97 | empty |
| 4 | 478 | 0.76 | 0.84 | 73 | empty |
| 5 | 602 | 0.75 | 0.82 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5382 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 5114 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 4324 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 34 glycan (disulfide, N-glycosylation).
Compared structures
- 7LWM · Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up… · the same entry in another collection · chain B against B, 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 7LWM · PDBe 7LWM · UniProt P0DTC2
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