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Crystal structure of the human coronavirus SARS HR1 motif in complex with pan-covs inhibitor EK1
Analyse Crystal structure of the human coronavirus SARS HR1 motif 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
- 5ZVM
- Type
- protein
- Length
- 309 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Pan-cov inhibitory peptide EK1
- UniProt
- P59594
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 69 | 97% helix, 0% strand | P59594 |
| B | Spike glycoprotein | protein | 76 | 95% helix, 0% strand | P59594 |
| C | Spike glycoprotein | protein | 67 | 97% helix, 0% strand | P59594 |
| a | Pan-cov inhibitory peptide EK1 | protein | 29 | 52% helix, 0% strand | — |
| b | Pan-cov inhibitory peptide EK1 | protein | 35 | 43% helix, 0% strand | — |
| c | Pan-cov inhibitory peptide EK1 | protein | 33 | 48% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.74 | 0.99 | 16 | empty |
| 2 | 103 | 0.56 | 0.83 | 16 | empty |
| 3 | 58 | 0.31 | 0.75 | 13 | empty |
Interfaces
9 interfaces between chains.
- C–b · 1199 Ų buried · 15 hydrogen bonds · protein-protein
- B–b · 1109 Ų buried · 9 hydrogen bonds · protein-protein
- A–c · 1076 Ų buried · 12 hydrogen bonds · protein-protein
- C–c · 1073 Ų buried · 10 hydrogen bonds · protein-protein
- A–a · 992 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5ZVM · Crystal Structure of the Human Coronavirus SARS HR1 motif in complex with pan-CoVs… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.21
- 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 0.21
- 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 0.20
- 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 0.20
- 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 0.20
- 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 0.20
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 5ZVM · PDBe 5ZVM · UniProt P59594
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