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Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with fi-3A and fd-11A fabs
Analyse Crystal structure of the receptor binding domain of SARS-cov-2 spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PQZ
- Type
- protein
- Length
- 1,059 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Fi-3A Fab heavy chain; Fi-3A Fab light chain; Fd-11A Fab heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG, PO4
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 189 | 12% helix, 29% strand | P0DTC2 |
| H | Fi-3A Fab heavy chain | protein | 217 | 5% helix, 49% strand | — |
| L | Fi-3A Fab light chain | protein | 213 | 5% helix, 50% strand | — |
| A | Fd-11A Fab heavy chain | protein | 225 | 5% helix, 48% strand | — |
| B | Fd-11A Fab light chain | protein | 215 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, B
- PO4 · Phosphate ion · ion · 2 copies · chains E, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.68 | 0.81 | 48 | PO4 |
| 2 | 568 | 0.60 | 0.73 | 58 | empty |
| 3 | 291 | 0.52 | 0.74 | 36 | empty |
| 4 | 150 | 0.44 | 0.75 | 28 | empty |
| 5 | 155 | 0.42 | 0.74 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1797 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1725 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 771 Ų buried · 20 hydrogen bonds · protein-protein
- E–A · 566 Ų buried · 7 hydrogen bonds · protein-protein
- E–L · 294 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7PQZ · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in… · the same entry in another collection · chain E against E, 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 7PQZ · PDBe 7PQZ · UniProt P0DTC2
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