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Crystal structure of murine norovirus P domain in complex with Nanobody NB-5829 and glycochenodeoxycholate (GCDCA)
Analyse Crystal structure of murine norovirus P domain in complex with Nanobody NB-5829… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XW7
- Type
- protein
- Length
- 1,677 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Murine norovirus 1; Vicugna pacos
- Molecule
- Capsid protein; Nanobody NB-5829
- UniProt
- Q80J94
- Ligands
- CHO, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.15 · 6 distinct chains · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 303 | 6% helix, 39% strand | Q80J94 |
| B | Capsid protein | protein | 305 | 6% helix, 38% strand | Q80J94 |
| E | Capsid protein | protein | 303 | 5% helix, 40% strand | Q80J94 |
| F | Capsid protein | protein | 301 | 6% helix, 39% strand | Q80J94 |
| C, D, G | Nanobody NB-5829 | protein | 117 | 10% helix, 53% strand | — |
| H | Nanobody NB-5829 | protein | 114 | 5% helix, 46% strand | — |
Ligands and binding sites
- CHO · Glycochenodeoxycholic acid · ligand · 4 copies · chains A, B, E, F
- MG · Magnesium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, E, C, B, D, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.79 | 0.96 | 35 | empty |
| 2 | 144 | 0.79 | 0.96 | 32 | empty |
| 3 | 385 | 0.70 | 0.82 | 55 | empty |
| 4 | 450 | 0.68 | 0.80 | 57 | empty |
| 5 | 209 | 0.67 | 0.85 | 45 | EDO |
Interfaces
13 interfaces between chains.
- E–F · 2017 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2003 Ų buried · 40 hydrogen bonds · protein-protein
- E–G · 878 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 843 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 833 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6XW7 · Crystal structure of murine norovirus P domain in complex with nanobody nb-5829 and… · 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 6XW7 · PDBe 6XW7 · UniProt Q80J94
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