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Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C135
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
- 7K8Z
- Type
- protein
- Length
- 3,335 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C135 Fab heavy chain; C135 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 967 | 24% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 949 | 23% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 972 | 24% helix, 32% strand | P0DTC2 |
| H | C135 Fab heavy chain | protein | 118 | 10% helix, 47% strand | — |
| L, N | C135 Fab light chain | protein | 106 | 3% helix, 47% strand | — |
| M | C135 Fab heavy chain | protein | 117 | 10% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, 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 | 905 | 0.85 | 0.87 | 110 | empty |
| 2 | 413 | 0.83 | 0.91 | 54 | empty |
| 3 | 429 | 0.82 | 0.90 | 51 | empty |
| 4 | 658 | 0.82 | 0.87 | 98 | empty |
| 5 | 391 | 0.77 | 0.86 | 35 | empty |
Interfaces
11 interfaces between chains.
- A–C · 5051 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 4490 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4032 Ų buried · 34 hydrogen bonds · protein-protein
- M–N · 835 Ų buried · 3 hydrogen bonds · protein-protein
- H–L · 803 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7K8Z · 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 7K8Z · PDBe 7K8Z · UniProt P0DTC2
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