MolNFT v1 · #187400 · protein
Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, R40-1G8
7SC1 · Spike glycoprotein: “Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, R40-1G8”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #187400 on…
- PDB
- 7SC1
- Type
- protein
- Length
- 3,705 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; R40-1G8 Fab heavy chain; R40-1G8 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1011 | 22% helix, 28% strand | P0DTC2 |
| H, M, P | R40-1G8 Fab heavy chain | protein | 117 | 8% helix, 34% strand | — |
| L, N, Q | R40-1G8 Fab light chain | protein | 107 | 0% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.85 | 0.87 | 97 | empty |
| 2 | 840 | 0.85 | 0.87 | 116 | empty |
| 3 | 113 | 0.77 | 0.97 | 22 | empty |
| 4 | 739 | 0.76 | 0.81 | 58 | empty |
| 5 | 573 | 0.74 | 0.82 | 38 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4490 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 4490 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 4445 Ų buried · 28 hydrogen bonds · protein-protein
- P–Q · 845 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 844 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SC1 · Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody… · 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 7SC1 · PDBe 7SC1 · UniProt P0DTC2
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