MolNFT v1 · #186323 · protein
SARS-cov-2 S glycoprotein in complex with S2X259 Fab
7RA8 · Spike glycoprotein: “SARS-cov-2 S glycoprotein in complex with S2X259 Fab”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #186323 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RA8
- Type
- protein
- Length
- 3,405 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain Fab S2X259 Fab variable domain; Light chain Fab S2X259…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 917 | 25% helix, 33% strand | P0DTC2 |
| H, C, F | Heavy chain Fab S2X259 Fab variable domain | protein | 119 | 5% helix, 49% strand | — |
| L, D, G | Light chain Fab S2X259 Fab variable domain | protein | 99 | 0% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains A, B, E
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 | 1138 | 0.85 | 0.86 | 140 | empty |
| 2 | 1106 | 0.85 | 0.86 | 143 | empty |
| 3 | 1127 | 0.85 | 0.86 | 140 | empty |
| 4 | 1151 | 0.85 | 0.85 | 122 | empty |
| 5 | 1138 | 0.83 | 0.84 | 122 | empty |
Interfaces
12 interfaces between chains.
- B–E · 4039 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 4026 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 4018 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 367 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 366 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7RA8 · SARS-CoV-2 S glycoprotein in complex with S2X259 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 7RA8 · PDBe 7RA8 · UniProt P0DTC2
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