MolNFT v1 · #191466 · protein
Structure of SARS-cov-2 omicron BA.1.1.529 spike trimer with one rbd down in complex with the Fab fragment of human neutralizing antibody MB.02
8DZI · Spike glycoprotein: “Structure of SARS-cov-2 omicron BA.1.1.529 spike trimer with one rbd down in complex with the Fab fragment of…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #191466 on…
- PDB
- 8DZI
- Type
- protein
- Length
- 3,918 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 · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 1083 | 22% helix, 29% strand | P0DTC2 |
| H, B, G | Antibody MB.02 heavy chain | protein | 118 | 3% helix, 31% strand | — |
| L, D, F | Antibody MB.02 light chain | protein | 109 | 0% helix, 29% strand | — |
| A | Spike glycoprotein | protein | 1080 | 22% helix, 31% strand | P0DTC2 |
| E | Spike glycoprotein | protein | 1074 | 22% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains C, E, A
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 | 1107 | 0.87 | 0.88 | 87 | empty |
| 2 | 830 | 0.85 | 0.87 | 106 | empty |
| 3 | 1072 | 0.83 | 0.84 | 108 | empty |
| 4 | 642 | 0.83 | 0.87 | 79 | empty |
| 5 | 758 | 0.82 | 0.85 | 81 | empty |
Interfaces
12 interfaces between chains.
- A–E · 5280 Ų buried · 64 hydrogen bonds · protein-protein
- C–E · 4264 Ų buried · 38 hydrogen bonds · protein-protein
- C–A · 4204 Ų buried · 46 hydrogen bonds · protein-protein
- H–L · 670 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 633 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 41 glycan (disulfide, N-glycosylation).
Compared structures
- 8DZI · Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with one RBD down in complex with… · the same entry in another collection · chain G against G, 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 8DZI · PDBe 8DZI · UniProt P0DTC2
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