MolNFT v1 · #184917 · protein
SARS-cov-2 spike protein in complex with SYBODYB#15 in a 1UP/1UP- OUT/1DOWN conformation.
7P79 · Spike glycoprotein: “SARS-cov-2 spike protein in complex with SYBODYB#15 in a 1UP/1UP- OUT/1DOWN conformation.”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #184917 on GenesisL1: 3D…
- PDB
- 7P79
- Type
- protein
- Length
- 3,377 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; SYBODY#15
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | Spike glycoprotein | protein | 1036 | 21% helix, 28% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 963 | 22% helix, 30% strand | P0DTC2 |
| B, D, H | SYBODY#15 | protein | 114 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 49 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains E, 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 | 1145 | 0.87 | 0.88 | 144 | empty |
| 2 | 351 | 0.80 | 0.90 | 32 | empty |
| 3 | 504 | 0.80 | 0.87 | 59 | empty |
| 4 | 965 | 0.79 | 0.81 | 88 | empty |
| 5 | 319 | 0.77 | 0.88 | 45 | empty |
Interfaces
7 interfaces between chains.
- C–A · 4806 Ų buried · 44 hydrogen bonds · protein-protein
- E–A · 4302 Ų buried · 37 hydrogen bonds · protein-protein
- C–E · 4086 Ų buried · 43 hydrogen bonds · protein-protein
- C–B · 1071 Ų buried · 10 hydrogen bonds · protein-protein
- E–D · 1037 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 34 glycan (disulfide, N-glycosylation, glycosylation, O-glycosylation).
Compared structures
- 7P79 · SARS-CoV-2 spike protein in complex with sybodyb#15 in a 1up/1up-out/1down conformation. · the same entry in another collection · chain C against C, 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 7P79 · PDBe 7P79 · UniProt P0DTC2
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