Research workbench
Crystal structure of murine norovirus P domain in complex with nanobody nb-5867
Analyse Crystal structure of murine norovirus P domain in complex with nanobody nb-5867 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XW4
- Type
- protein
- Length
- 847 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nanobody nb-5867
- UniProt
- Q80J94
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Capsid protein | protein | 302 | 6% helix, 40% strand | Q80J94 |
| C | Nanobody nb-5867 | protein | 121 | 5% helix, 50% strand | — |
| D | Nanobody nb-5867 | protein | 122 | 5% helix, 49% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.81 | 0.97 | 34 | EDO |
| 2 | 252 | 0.64 | 0.82 | 34 | EDO |
| 3 | 265 | 0.64 | 0.81 | 31 | EDO |
| 4 | 360 | 0.53 | 0.73 | 61 | empty |
| 5 | 81 | 0.37 | 0.77 | 18 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 1918 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 971 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 952 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 85 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 79 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6XW4 · Crystal structure of murine norovirus P domain in complex with Nanobody NB-5867 · 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 6XW4 · PDBe 6XW4 · UniProt Q80J94
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