Research workbench
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with fd-5D Fab
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
- 7PR0
- Type
- protein
- Length
- 1,892 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Fd-5D Fab light chain; Fd-5D Fab heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG, SO4, NO3, CL
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, D | Spike protein S1 | protein | 197 | 17% helix, 29% strand | P0DTC2 |
| L | Fd-5D Fab light chain | protein | 221 | 5% helix, 50% strand | — |
| H | Fd-5D Fab heavy chain | protein | 228 | 7% helix, 49% strand | — |
| A | Spike protein S1 | protein | 199 | 16% helix, 29% strand | P0DTC2 |
| B | Fd-5D Fab light chain | protein | 219 | 5% helix, 50% strand | — |
| C | Fd-5D Fab heavy chain | protein | 223 | 8% helix, 49% strand | — |
| F | Fd-5D Fab light chain | protein | 217 | 6% helix, 49% strand | — |
| G | Fd-5D Fab heavy chain | protein | 191 | 6% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E, A, D
- SO4 · Sulfate ion · ion · 3 copies · chains E, L, H
- NO3 · Nitrate ion · ion · 3 copies · chains L, H, C
- CL · Chloride ion · ion · 3 copies · chains L, E, H, D, F, G
- GOL · Glycerol · additive · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.73 | 0.76 | 106 | empty |
| 2 | 541 | 0.66 | 0.77 | 65 | SO4 |
| 3 | 150 | 0.58 | 0.82 | 22 | empty |
| 4 | 84 | 0.57 | 0.87 | 23 | empty |
| 5 | 231 | 0.54 | 0.77 | 23 | empty |
Interfaces
15 interfaces between chains.
- L–H · 1955 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1723 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1603 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 830 Ų buried · 14 hydrogen bonds · protein-protein
- E–A · 710 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7PR0 · 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 7PR0 · PDBe 7PR0 · UniProt P0DTC2
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