Research workbench
Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C002 (state 2)
Analyse Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K8T
- Type
- protein
- Length
- 3,699 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C002 Fab heavy chain; C002 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1001 | 23% helix, 31% strand | P0DTC2 |
| H, M, O | C002 Fab heavy chain | protein | 125 | 7% helix, 46% strand | — |
| L, N, P | C002 Fab light chain | protein | 107 | 3% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, B, C, P
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 | 1105 | 0.87 | 0.89 | 129 | empty |
| 2 | 879 | 0.87 | 0.89 | 109 | empty |
| 3 | 1003 | 0.82 | 0.83 | 132 | NAG |
| 4 | 963 | 0.81 | 0.83 | 97 | empty |
| 5 | 613 | 0.78 | 0.84 | 52 | empty |
Interfaces
15 interfaces between chains.
- A–C · 4846 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 4594 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 4426 Ų buried · 44 hydrogen bonds · protein-protein
- H–L · 872 Ų buried · 5 hydrogen bonds · protein-protein
- A–O · 836 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7K8T · 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 7K8T · PDBe 7K8T · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.