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Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121 (state 2)
Analyse Structure of the SARS-cov-2 S 2P 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
- 7K8Y
- Type
- protein
- Length
- 3,242 residues
- Chains
- 5
- 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 0.85
Structure
electron microscopy · 3 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, E | Spike glycoprotein | protein | 1002 | 22% helix, 32% strand | P0DTC2 |
| G | C121 Fab heavy chain | protein | 128 | 5% helix, 45% strand | — |
| I | C121 Fab light chain | protein | 108 | 3% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains B, E, D
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 | 1194 | 0.85 | 0.86 | 149 | empty |
| 2 | 469 | 0.83 | 0.90 | 74 | empty |
| 3 | 841 | 0.81 | 0.83 | 96 | empty |
| 4 | 476 | 0.79 | 0.86 | 62 | empty |
| 5 | 631 | 0.78 | 0.83 | 53 | empty |
Interfaces
7 interfaces between chains.
- B–D · 4502 Ų buried · 53 hydrogen bonds · protein-protein
- B–E · 4253 Ų buried · 50 hydrogen bonds · protein-protein
- D–E · 4062 Ų buried · 49 hydrogen bonds · protein-protein
- B–G · 780 Ų buried · 3 hydrogen bonds · protein-protein
- G–I · 745 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 24 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7K8Y · Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody… · the same entry in another collection · chain B against B, 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 7K8Y · PDBe 7K8Y · UniProt P0DTC2
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