Research workbench
Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R
Analyse Crystal structure of SARS spike protein receptor binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GHW
- Type
- protein
- Length
- 842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Anti-SARS scfv antibody, 80R
- UniProt
- P59594, Q65ZC9
- Ligands
- CL
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 191 | 17% helix, 32% strand | P59594 |
| B | Anti-SARS scfv antibody, 80R | protein | 232 | 4% helix, 50% strand | Q65ZC9 |
| C | Spike glycoprotein | protein | 188 | 16% helix, 32% strand | P59594 |
| D | Anti-SARS scfv antibody, 80R | protein | 231 | 5% helix, 50% strand | Q65ZC9 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.60 | 0.83 | 26 | empty |
| 2 | 234 | 0.53 | 0.77 | 40 | CL |
| 3 | 64 | 0.51 | 0.86 | 19 | empty |
| 4 | 140 | 0.49 | 0.79 | 22 | empty |
| 5 | 76 | 0.34 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1213 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1209 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 662 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 2GHW · Crystal structure of SARS spike protein receptor binding domain in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.89
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.89
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.88
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 P59594
- Every structure of UniProt Q65ZC9
- Elsewhere: RCSB PDB 2GHW · PDBe 2GHW · UniProt P59594 · UniProt Q65ZC9
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