MolNFT v1 · #190248 · protein
SARS-cov-2 omicron variant S trimer complexed with one JMB2002 Fab
7WPD · Spike glycoprotein: “SARS-cov-2 omicron variant S trimer complexed with one JMB2002 Fab”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #190248 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7WPD
- Type
- protein
- Length
- 3,628 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; JMB2002 Fab heavy chain; JMB2002 Fab light chian; Anti-Fab nanobody
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1024 | 22% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1024 | 22% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1022 | 22% helix, 31% strand | P0DTC2 |
| X | JMB2002 Fab heavy chain | protein | 225 | 7% helix, 49% strand | — |
| Y | JMB2002 Fab light chian | protein | 213 | 8% helix, 50% strand | — |
| Z | Anti-Fab nanobody | protein | 120 | 0% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 37 copies · chains A, C, B
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 | 849 | 0.84 | 0.86 | 106 | empty |
| 2 | 1177 | 0.83 | 0.84 | 123 | empty |
| 3 | 774 | 0.81 | 0.85 | 84 | empty |
| 4 | 674 | 0.81 | 0.85 | 77 | empty |
| 5 | 453 | 0.76 | 0.85 | 49 | empty |
Interfaces
7 interfaces between chains.
- A–C · 4492 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 4312 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 3837 Ų buried · 25 hydrogen bonds · protein-protein
- X–Y · 1246 Ų buried · 3 hydrogen bonds · protein-protein
- Y–Z · 607 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide, 35 glycan (disulfide, N-glycosylation).
Compared structures
- 7WPD · SARS-CoV-2 Omicron Variant S Trimer complexed with one JMB2002 Fab · 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 7WPD · PDBe 7WPD · UniProt P0DTC2
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