Research workbench
SARS-cov complex with human neutralizing S230 antibody Fab fragment (state 1)
Analyse SARS-cov complex with human neutralizing S230 antibody Fab fragment (state 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NB6
- Type
- protein
- Length
- 3,599 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S230 heavy chain; S230 light chain
- UniProt
- P59594
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 7 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1052 | 22% helix, 35% strand | P59594 |
| B | Spike glycoprotein | protein | 1026 | 22% helix, 36% strand | P59594 |
| C | Spike glycoprotein | protein | 1055 | 22% helix, 35% strand | P59594 |
| H | S230 heavy chain | protein | 123 | 10% helix, 46% strand | — |
| I | S230 heavy chain | protein | 124 | 10% helix, 45% strand | — |
| L | S230 light chain | protein | 110 | 3% helix, 52% strand | — |
| M | S230 light chain | protein | 109 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 37 copies
- MAN · alpha-D-mannopyranose · sugar · 19 copies
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 | 896 | 0.89 | 0.92 | 106 | empty |
| 2 | 868 | 0.85 | 0.87 | 87 | empty |
| 3 | 1130 | 0.80 | 0.81 | 114 | empty |
| 4 | 1101 | 0.79 | 0.81 | 141 | empty |
| 5 | 1023 | 0.78 | 0.80 | 115 | empty |
Interfaces
10 interfaces between chains.
- A–C · 4495 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3936 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3714 Ų buried · 32 hydrogen bonds · protein-protein
- I–M · 363 Ų buried · 0 hydrogen bonds · protein-protein
- H–L · 346 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 55 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 6NB6 · SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 1) · the same entry in another collection · chain A against A, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.16
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.16
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.16
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.16
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 P59594
- Elsewhere: RCSB PDB 6NB6 · PDBe 6NB6 · UniProt P59594
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