Research workbench
Mouse norovirus complexed with gcdca
Analyse Mouse norovirus complexed with gcdca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P4J
- Type
- protein
- Length
- 1,529 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q2V8W4
- Ligands
- CHO
- Pockets
- 9 · best druggability 0.63
Structure
electron microscopy · 3 distinct chains · 3% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 514 | 2% helix, 33% strand | Q2V8W4 |
| B | Capsid protein | protein | 513 | 3% helix, 32% strand | Q2V8W4 |
| C | Capsid protein | protein | 502 | 5% helix, 31% strand | Q2V8W4 |
Ligands and binding sites
- CHO · Glycochenodeoxycholic acid · ligand · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.63 | 0.76 | 57 | empty |
| 2 | 304 | 0.61 | 0.79 | 43 | empty |
| 3 | 252 | 0.55 | 0.77 | 26 | empty |
| 4 | 288 | 0.54 | 0.75 | 24 | empty |
| 5 | 121 | 0.51 | 0.81 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1185 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 872 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 870 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6P4J · Mouse norovirus complexed with GCDCA · the same entry in another collection · chain A against A, 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 Q2V8W4
- Elsewhere: RCSB PDB 6P4J · PDBe 6P4J · UniProt Q2V8W4
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