Research workbench
Down-state locked, S2 stabilized RS2D-hexapro SARS-cov-2 spike ectodomain in the rbd-down conformation, state 2
Analyse Down-state locked, S2 stabilized RS2D-hexapro SARS-cov-2 spike ectodomain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TLD
- Type
- protein
- Length
- 2,916 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 972 | 24% helix, 34% strand | P0DTC2 |
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 | 829 | 0.86 | 0.88 | 100 | empty |
| 2 | 680 | 0.85 | 0.89 | 100 | empty |
| 3 | 979 | 0.82 | 0.84 | 101 | empty |
| 4 | 636 | 0.82 | 0.87 | 81 | empty |
| 5 | 448 | 0.77 | 0.85 | 52 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5485 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 5278 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 4976 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide (disulfide).
Compared structures
- 7TLD · Down-state locked, S2 stabilized rS2d-HexaPro SARS-CoV-2 spike ectodomain in the 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 7TLD · PDBe 7TLD · UniProt P0DTC2
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