Research workbench
SARS-cov-2 spike in complex with the S2H13 neutralizing antibody (one rbd open)
Analyse SARS-cov-2 spike in complex with the S2H13 neutralizing antibody (one rbd open) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JV4
- Type
- protein
- Length
- 3,568 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2H13 Fab heavy chain; S2H13 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 975 | 23% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 949 | 22% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 963 | 23% helix, 33% strand | P0DTC2 |
| H, F, D | S2H13 Fab heavy chain | protein | 118 | 3% helix, 49% strand | — |
| L, G, E | S2H13 Fab light chain | protein | 109 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 58 copies · chains A, B, 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 | 783 | 0.86 | 0.89 | 94 | empty |
| 2 | 1117 | 0.85 | 0.86 | 145 | empty |
| 3 | 767 | 0.84 | 0.87 | 83 | empty |
| 4 | 761 | 0.80 | 0.84 | 110 | empty |
| 5 | 513 | 0.79 | 0.86 | 52 | empty |
Interfaces
14 interfaces between chains.
- A–C · 4473 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 4373 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 3829 Ų buried · 31 hydrogen bonds · protein-protein
- H–L · 456 Ų buried · 0 hydrogen bonds · protein-protein
- F–G · 453 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7JV4 · SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody (one RBD open) · 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 7JV4 · PDBe 7JV4 · UniProt P0DTC2
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