Research workbench
The complex structure of omicron BA.1 rbd with BD604, S309,AND S304
Analyse The complex structure of omicron BA.1 rbd with BD604, S309,AND S304 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X1M
- Type
- protein
- Length
- 1,291 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S309 Fab heavy chain; S309 Fab light chain; Bd-604 Fab heavy chain; Bd-604 Fab light…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 13 · best druggability 0.75
Structure
electron microscopy · 7 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S309 Fab heavy chain | protein | 225 | 4% helix, 45% strand | — |
| B | S309 Fab light chain | protein | 212 | 6% helix, 44% strand | — |
| C | Bd-604 Fab heavy chain | protein | 219 | 4% helix, 48% strand | — |
| D | Bd-604 Fab light chain | protein | 213 | 5% helix, 42% strand | — |
| H | S304 Fab haavy chain | protein | 119 | 3% helix, 57% strand | — |
| L | S304 Fab light chain | protein | 108 | 0% helix, 53% strand | — |
| M | Spike protein S1 | protein | 195 | 16% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, M
- FUC · alpha-L-fucopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.75 | 0.91 | 34 | empty |
| 2 | 418 | 0.65 | 0.79 | 56 | empty |
| 3 | 346 | 0.55 | 0.74 | 46 | empty |
| 4 | 73 | 0.54 | 0.87 | 19 | empty |
| 5 | 339 | 0.54 | 0.74 | 41 | NAG, FUC |
Interfaces
9 interfaces between chains.
- C–D · 1862 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1597 Ų buried · 6 hydrogen bonds · protein-protein
- H–L · 902 Ų buried · 6 hydrogen bonds · protein-protein
- C–M · 790 Ų buried · 9 hydrogen bonds · protein-protein
- A–M · 689 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7X1M · The complex structure of Omicron BA.1 RBD with BD604, S309,and S304 · 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 7X1M · PDBe 7X1M · UniProt P0DTC2
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