MolNFT v1 · #179548 · protein
Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121 (state 1)
7K8X · Spike glycoprotein: “Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #179548 on…
- PDB
- 7K8X
- Type
- protein
- Length
- 3,478 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C121 Fab heavy chain; C121 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1002 | 22% helix, 33% strand | P0DTC2 |
| D, E | C121 Fab heavy chain | protein | 128 | 2% helix, 45% strand | — |
| F, G | C121 Fab light chain | protein | 108 | 3% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.83 | 0.88 | 79 | empty |
| 2 | 404 | 0.82 | 0.90 | 63 | empty |
| 3 | 793 | 0.81 | 0.84 | 75 | empty |
| 4 | 661 | 0.80 | 0.84 | 80 | empty |
| 5 | 124 | 0.78 | 0.96 | 27 | empty |
Interfaces
11 interfaces between chains.
- B–C · 4596 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 4545 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 4236 Ų buried · 46 hydrogen bonds · protein-protein
- E–G · 796 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 788 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide, 28 glycan (disulfide, N-glycosylation, glycation).
Compared structures
- 7K8X · Structure of the SARS-CoV-2 S 2P 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 7K8X · PDBe 7K8X · UniProt P0DTC2
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