Research workbench
X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab
Analyse X-ray crystal structure of the SARS coronavirus spike receptor binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BGF
- Type
- protein
- Length
- 1,211 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; F26G19 Fab
- UniProt
- P59594
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Spike protein S1 | protein | 179 | 16% helix, 27% strand | P59594 |
| A | Spike protein S1 | protein | 178 | 14% helix, 27% strand | P59594 |
| L | F26G19 Fab | protein | 212 | 6% helix, 53% strand | — |
| H, B | F26G19 Fab | protein | 216 | 7% helix, 53% strand | — |
| C | F26G19 Fab | protein | 210 | 6% helix, 52% strand | — |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.71 | 0.77 | 63 | empty |
| 2 | 683 | 0.70 | 0.77 | 59 | empty |
| 3 | 396 | 0.55 | 0.74 | 54 | empty |
| 4 | 341 | 0.54 | 0.74 | 45 | empty |
| 5 | 98 | 0.51 | 0.82 | 31 | empty |
Interfaces
8 interfaces between chains.
- C–B · 1935 Ų buried · 19 hydrogen bonds · protein-protein
- L–H · 1919 Ų buried · 21 hydrogen bonds · protein-protein
- S–A · 710 Ų buried · 12 hydrogen bonds · protein-protein
- S–H · 621 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 620 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 3BGF · X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex… · the same entry in another collection · chain B against B, 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 A against E, TM-score 0.94
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.93
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.93
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
- Elsewhere: RCSB PDB 3BGF · PDBe 3BGF · UniProt P59594
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