Research workbench
Crystal structure of capsid P domain of norovirus GI.3 VA115 complexed with GALA1-3GALB1-4GLC
Analyse Crystal structure of capsid P domain of norovirus GI.3 VA115 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ER1
- Type
- protein
- Length
- 1,206 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid P domain
- Ligands
- GAL, GLA
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Capsid P domain | protein | 303 | 9% helix, 33% strand | — |
| C | Capsid P domain | protein | 300 | 9% helix, 34% strand | — |
| D | Capsid P domain | protein | 300 | 9% helix, 32% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.80 | 0.91 | 46 | empty |
| 2 | 277 | 0.80 | 0.92 | 55 | empty |
| 3 | 1143 | 0.76 | 0.79 | 104 | empty |
| 4 | 69 | 0.71 | 0.97 | 20 | empty |
| 5 | 65 | 0.70 | 0.97 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1824 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1823 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 561 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 515 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 219 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7ER1 · Crystal structure of capsid P domain of norovirus GI.3 VA115 complexed with… · 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
- Elsewhere: RCSB PDB 7ER1 · PDBe 7ER1
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