MolNFT v1 · #186336 · protein
SARS-cov-2 S bound to S2X259 Fab (local refinement of the RBD/S2X259 variable domains)
7RAL · S2X259 Fab heavy chain: “SARS-cov-2 S bound to S2X259 Fab (local refinement of the RBD/S2X259 variable domains)”. Electron microscopy, 1 ligand (NAG), 5 pockets (best druggability 0.54). MolNFT v1 #186336 on GenesisL1: 3D structure…
- PDB
- 7RAL
- Type
- protein
- Length
- 389 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S2X259 Fab heavy chain; S2X259 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.54
Structure
electron microscopy · 3 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S2X259 Fab heavy chain | protein | 119 | 5% helix, 49% strand | — |
| L | S2X259 Fab light chain | protein | 99 | 0% helix, 46% strand | — |
| B | Spike glycoprotein | protein | 171 | 17% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.54 | 0.82 | 29 | empty |
| 2 | 92 | 0.47 | 0.81 | 21 | empty |
| 3 | 125 | 0.46 | 0.78 | 28 | empty |
| 4 | 94 | 0.36 | 0.75 | 18 | empty |
| 5 | 72 | 0.32 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 871 Ų buried · 9 hydrogen bonds · protein-protein
- H–B · 677 Ų buried · 11 hydrogen bonds · protein-protein
- L–B · 319 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7RAL · SARS-CoV-2 S bound to S2X259 Fab (local refinement of the RBD/S2X259 variable domains) · the same entry in another collection · chain H against H, 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 7RAL · PDBe 7RAL · UniProt P0DTC2
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