Research workbench
Down-state locked RS2D SARS-cov-2 spike ectodomain in the rbd-down conformation, state 1
Analyse Down-state locked RS2D SARS-cov-2 spike ectodomain in the rbd-down… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TLA
- Type
- protein
- Length
- 2,948 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 972 | 24% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 992 | 24% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 984 | 24% helix, 33% 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 | 943 | 0.84 | 0.86 | 110 | empty |
| 2 | 673 | 0.84 | 0.88 | 90 | empty |
| 3 | 1048 | 0.83 | 0.84 | 104 | empty |
| 4 | 920 | 0.81 | 0.83 | 108 | empty |
| 5 | 178 | 0.79 | 0.94 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5840 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 5645 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 5404 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide (disulfide).
Compared structures
- 7TLA · Down-state locked rS2d SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 1 · 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 7TLA · PDBe 7TLA · UniProt P0DTC2
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