Research workbench
Crystal structure of murine norovirus P domain in complex with nanobody nb-5853
Analyse Crystal structure of murine norovirus P domain in complex with nanobody nb-5853 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XW6
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nanobody nb-5853
- UniProt
- Q80J94
- Ligands
- MG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Capsid protein | protein | 304 | 5% helix, 39% strand | Q80J94 |
| D, C | Nanobody nb-5853 | protein | 126 | 7% helix, 48% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.80 | 0.96 | 37 | empty |
| 2 | 242 | 0.63 | 0.82 | 32 | empty |
| 3 | 522 | 0.62 | 0.75 | 83 | empty |
| 4 | 240 | 0.60 | 0.80 | 32 | empty |
| 5 | 89 | 0.34 | 0.73 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1970 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 864 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 816 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 102 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6XW6 · Crystal structure of murine norovirus P domain in complex with Nanobody NB-5853 · 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 Q80J94
- Elsewhere: RCSB PDB 6XW6 · PDBe 6XW6 · UniProt Q80J94
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