Research workbench
SARS-cov-2 omicron BA.2 variant spike trimer with three JMB2002 Fab bound
Analyse SARS-cov-2 omicron BA.2 variant spike trimer with three JMB2002 Fab bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XOD
- Type
- protein
- Length
- 4,742 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of JMB2002 Fab; Light chain of JMB2002 Fab; Nanobody
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1026 | 22% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1025 | 21% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1024 | 22% helix, 30% strand | P0DTC2 |
| X | Heavy chain of JMB2002 Fab | protein | 222 | 6% helix, 45% strand | — |
| Y, S | Light chain of JMB2002 Fab | protein | 213 | 8% helix, 47% strand | — |
| Z, W, T | Nanobody | protein | 120 | 5% helix, 44% strand | — |
| U, R | Heavy chain of JMB2002 Fab | protein | 224 | 5% helix, 47% strand | — |
| V | Light chain of JMB2002 Fab | protein | 211 | 8% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, 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 | 1067 | 0.84 | 0.85 | 114 | empty |
| 2 | 1149 | 0.82 | 0.83 | 121 | empty |
| 3 | 712 | 0.82 | 0.86 | 62 | empty |
| 4 | 627 | 0.79 | 0.85 | 100 | empty |
| 5 | 1191 | 0.79 | 0.81 | 122 | empty |
Interfaces
15 interfaces between chains.
- A–C · 4526 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 4163 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3870 Ų buried · 28 hydrogen bonds · protein-protein
- U–V · 1928 Ų buried · 9 hydrogen bonds · protein-protein
- X–Y · 1862 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 37 glycan (disulfide, N-glycosylation).
Compared structures
- 7XOD · SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with three JMB2002 Fab Bound · 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 7XOD · PDBe 7XOD · UniProt P0DTC2
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