Research workbench
Atomic structure of the murine norovirus protruding domain and SCD300LF receptor complex
Analyse Atomic structure of the murine norovirus protruding domain and SCD300LF… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OR7
- Type
- protein
- Length
- 701 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; CMRF35-like molecule 1
- UniProt
- A7YK37, Q6SJQ7
- Ligands
- NA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 297 | 6% helix, 39% strand | A7YK37 |
| B | Capsid protein | protein | 293 | 8% helix, 39% strand | A7YK37 |
| C | CMRF35-like molecule 1 | protein | 111 | 8% helix, 50% strand | Q6SJQ7 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.79 | 0.88 | 62 | empty |
| 2 | 271 | 0.61 | 0.80 | 31 | empty |
| 3 | 131 | 0.44 | 0.76 | 30 | empty |
| 4 | 64 | 0.32 | 0.75 | 21 | empty |
| 5 | 71 | 0.31 | 0.74 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1881 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 675 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5OR7 · Atomic structure of the murine norovirus protruding domain and sCD300lf receptor complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q6SJQ7 · AlphaFold monomer V2.0 prediction for CMRF35-like molecule 1 (Q6SJQ7) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 A7YK37
- Every structure of UniProt Q6SJQ7
- Elsewhere: RCSB PDB 5OR7 · PDBe 5OR7 · UniProt A7YK37 · UniProt Q6SJQ7
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