MolNFT v1 · #179551 · protein
Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C144
7K90 · Spike glycoprotein: “Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C144”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #179551 on…
- PDB
- 7K90
- Type
- protein
- Length
- 3,711 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C144 Fab heavy chain; C144 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1000 | 20% helix, 28% strand | P0DTC2 |
| H, M, O | C144 Fab heavy chain | protein | 129 | 5% helix, 47% strand | — |
| L, N, P | C144 Fab light chain | protein | 108 | 0% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 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 | 958 | 0.87 | 0.89 | 134 | empty |
| 2 | 1052 | 0.82 | 0.83 | 114 | empty |
| 3 | 948 | 0.82 | 0.83 | 89 | empty |
| 4 | 1026 | 0.82 | 0.83 | 104 | empty |
| 5 | 1005 | 0.81 | 0.83 | 103 | empty |
Interfaces
18 interfaces between chains.
- B–C · 4893 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 4884 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 4863 Ų buried · 32 hydrogen bonds · protein-protein
- M–N · 980 Ų buried · 11 hydrogen bonds · protein-protein
- O–P · 966 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 33 glycan (disulfide, N-glycosylation).
Compared structures
- 7K90 · 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 7K90 · PDBe 7K90 · UniProt P0DTC2
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