Research workbench
SARS-cov-2 spike in complex with IgG 553-15 (S-553-15 dimer trimer )
Analyse SARS-cov-2 spike in complex with IgG 553-15 (S-553-15 dimer trimer ) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WO4
- Type
- protein
- Length
- 9,096 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; MAB15 vh; MAB15 vl
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, J, K, L | Spike glycoprotein | protein | 1076 | 19% helix, 28% strand | P0DTC2 |
| D, F, H, M, O, Q | MAB15 vh | protein | 225 | 1% helix, 39% strand | — |
| E, G, I, N, P, R | MAB15 vl | protein | 215 | 3% helix, 29% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 90 copies · chains A, B, C, J, K, L
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 | 1041 | 0.87 | 0.88 | 119 | empty |
| 2 | 723 | 0.86 | 0.89 | 90 | empty |
| 3 | 1058 | 0.85 | 0.86 | 107 | empty |
| 4 | 1073 | 0.82 | 0.83 | 97 | empty |
| 5 | 594 | 0.78 | 0.84 | 53 | empty |
Interfaces
33 interfaces between chains.
- K–L · 4032 Ų buried · 35 hydrogen bonds · protein-protein
- J–K · 3998 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 3993 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3968 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 3814 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 104 disulfide, 90 glycan (disulfide, N-glycosylation).
Compared structures
- 7WO4 · SARS-CoV-2 Spike in complex with IgG 553-15 (S-553-15 dimer trimer ) · 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 7WO4 · PDBe 7WO4 · UniProt P0DTC2
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