MolNFT v1 · #188106 · protein
Locally refined region of SARS-cov-2 spike in complex with antibody A19-46.1
7TC9 · Spike protein S1: “Locally refined region of SARS-cov-2 spike in complex with antibody A19-46.1”. Electron microscopy, 1 ligand (NAG), 15 pockets (best druggability 0.76). MolNFT v1 #188106 on GenesisL1: 3D structure, binding sites…
- PDB
- 7TC9
- Type
- protein
- Length
- 642 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Heavy chain of antibody A19-46.1; Light chain of antibody A19-46.1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 6% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike protein S1 | protein | 195 | 8% helix, 19% strand | P0DTC2 |
| H | Heavy chain of antibody A19-46.1 | protein | 231 | 4% helix, 35% strand | — |
| L | Light chain of antibody A19-46.1 | protein | 216 | 6% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.76 | 0.95 | 29 | empty |
| 2 | 187 | 0.73 | 0.89 | 37 | empty |
| 3 | 134 | 0.73 | 0.92 | 23 | empty |
| 4 | 66 | 0.71 | 0.96 | 20 | empty |
| 5 | 255 | 0.68 | 0.84 | 38 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1660 Ų buried · 11 hydrogen bonds · protein-protein
- B–L · 467 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 276 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7TC9 · Locally refined region of SARS-CoV-2 spike in complex with antibody A19-46.1 · 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 7TC9 · PDBe 7TC9 · UniProt P0DTC2
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