MolNFT v1 · #191465 · protein
Structure of SARS-cov-2 omicron BA.1.1.529 spike trimer with two rbds down in complex with the Fab fragment of human neutralizing antibody MB.02
8DZH · Spike glycoprotein: “Structure of SARS-cov-2 omicron BA.1.1.529 spike trimer with two rbds down in complex with the Fab fragment…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #191465 on…
- PDB
- 8DZH
- Type
- protein
- Length
- 3,966 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Antibody MB.02 heavy chain; Antibody MB.02 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike glycoprotein | protein | 1092 | 20% helix, 30% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1100 | 22% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1093 | 22% helix, 30% strand | P0DTC2 |
| E, H, I | Antibody MB.02 heavy chain | protein | 118 | 3% helix, 49% strand | — |
| D, L, J | Antibody MB.02 light chain | protein | 109 | 0% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 73 copies · chains B, 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 | 882 | 0.87 | 0.89 | 115 | empty |
| 2 | 1162 | 0.87 | 0.88 | 115 | empty |
| 3 | 942 | 0.84 | 0.86 | 111 | empty |
| 4 | 992 | 0.84 | 0.85 | 105 | empty |
| 5 | 752 | 0.83 | 0.86 | 89 | empty |
Interfaces
13 interfaces between chains.
- A–C · 5357 Ų buried · 56 hydrogen bonds · protein-protein
- B–A · 4922 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 4346 Ų buried · 48 hydrogen bonds · protein-protein
- H–L · 661 Ų buried · 3 hydrogen bonds · protein-protein
- E–D · 634 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 48 disulfide, 45 glycan (disulfide, N-glycosylation).
Compared structures
- 8DZH · Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with two RBDs down in complex… · 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 8DZH · PDBe 8DZH · UniProt P0DTC2
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