Research workbench
Trimeric SARS-cov-2 spike ectodomain bound to P008_056 Fab
Analyse Trimeric SARS-cov-2 spike ectodomain bound to P008_056 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NTC
- Type
- protein
- Length
- 3,698 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; P008_056 Fab heavy chain; P008_056 Fab light chain
- UniProt
- P0DTC2
- Ligands
- BLA, NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1087 | 20% helix, 29% strand | P0DTC2 |
| H | P008_056 Fab heavy chain | protein | 224 | 3% helix, 47% strand | — |
| L | P008_056 Fab light chain | protein | 213 | 5% helix, 46% strand | — |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 79 copies · chains A, B, 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 | 1047 | 0.88 | 0.89 | 110 | empty |
| 2 | 1028 | 0.84 | 0.85 | 116 | empty |
| 3 | 1183 | 0.83 | 0.84 | 147 | empty |
| 4 | 890 | 0.83 | 0.85 | 78 | empty |
| 5 | 1020 | 0.83 | 0.84 | 106 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4700 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 4655 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 4246 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 1470 Ų buried · 7 hydrogen bonds · protein-protein
- C–H · 803 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 55 glycan, 45 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7NTC · Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab · 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 7NTC · PDBe 7NTC · UniProt P0DTC2
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