Research workbench
3D model of the 3-rbd up single trimeric spike protein of SARS-COV2 in the presence of synthetic peptide sih-5.
Analyse 3D model of the 3-rbd up single trimeric spike protein of SARS-COV2 in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X7N
- Type
- protein
- Length
- 3,320 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Synthetic peptide sih-5
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 20% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike glycoprotein | protein | 1033 | 19% helix, 23% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1033 | 20% helix, 22% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1026 | 19% helix, 20% strand | P0DTC2 |
| D, E, H, I, F, G | Synthetic peptide sih-5 | protein | 38 | 79% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains B, A, 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 | 1045 | 0.82 | 0.83 | 138 | empty |
| 2 | 329 | 0.80 | 0.90 | 53 | empty |
| 3 | 359 | 0.78 | 0.88 | 43 | empty |
| 4 | 535 | 0.77 | 0.84 | 33 | empty |
| 5 | 246 | 0.76 | 0.89 | 40 | empty |
Interfaces
10 interfaces between chains.
- B–C · 4485 Ų buried · 34 hydrogen bonds · protein-protein
- B–A · 4375 Ų buried · 44 hydrogen bonds · protein-protein
- C–A · 4176 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 1276 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1086 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 glycan, 38 disulfide, 6 d-amino, 6 modified (N-glycosylation, disulfide, D-amino acid, nonstandard).
Compared structures
- 7X7N · 3D model of the 3-RBD up single trimeric spike protein of SARS-CoV2 in the presence of… · 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 7X7N · PDBe 7X7N · UniProt P0DTC2
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