Research workbench
Crystal structure of capsid P domain of norovirus GI.3 VA115
Analyse Crystal structure of capsid P domain of norovirus GI.3 VA115 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ER0
- Type
- protein
- Length
- 1,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid P domain
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid P domain | protein | 303 | 10% helix, 33% strand | — |
| B | Capsid P domain | protein | 300 | 9% helix, 32% strand | — |
| C | Capsid P domain | protein | 303 | 9% helix, 33% strand | — |
| D | Capsid P domain | protein | 302 | 9% helix, 33% strand | — |
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.79 | 0.91 | 57 | empty |
| 2 | 987 | 0.78 | 0.80 | 112 | empty |
| 3 | 162 | 0.72 | 0.90 | 30 | empty |
| 4 | 67 | 0.72 | 0.97 | 22 | empty |
| 5 | 136 | 0.71 | 0.91 | 36 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1796 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1780 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 534 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 496 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 219 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7ER0 · Crystal structure of capsid P domain of norovirus GI.3 VA115 · the same entry in another collection · chain D against D, 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 7ER0 · PDBe 7ER0
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